patser il22

This report summarizes the interaction of IL22 with 12 transcription factors: STAT03, CSLC, CSLH, CSLL, CMAF01, RORA1, AP1, STAT5A1, NFKappaB1, RORA2, STAT5A4, STAT5B1.

Patser/Conservation scores were generated with the formula: ∑k=i

i+ L ( ln((nk+ pk

N+1 ) 1pk

)´ ck), where i is the

position in the sequence, L is the length of the transcription factor binding site, nk is the kth element of the alignment matrix, pk is the fraction of each base in the genome (for each base, pb=0.25), and ck is the conservation score at position k, and N is the number of sequences being compared. These are the top 3 scores as determined by Patser, with their corresponding Patser/Conservation scores. The conservation scores and raw sequences were obtained from the UCSC Genome Browser. The logos were generated by enoLOGOS at http://www.benoslab.pitt.edu/cgi-bin/enologos/enologos.cgi. These scores were compiled in accordance to the highest Patser scores.

STAT03 (12.03)Frequency Matrix: A 20 13 38 6 321 8 6 585 606 191 C 19 10 552 541 21 0 2 21 1 15 G 25 129 9 1 148 605 592 7 5 393 T 549 461 14 65 123 0 13 0 1 14Sequece Logo:

Putative Sites:1)

Site: 117625169C Patser: 12.03

Cons/Pat: 0.84

Mouse TTCCAGGAAGHuman TTCCAGTAAARat TTCTGAGAAADog ==========

2)Site: 117622444 Patser:

9.80Cons/Pat: 0.84

Mouse TGCCTGGAAGHuman AGCCAGAAGGRat ==========Dog ==========

Site: 117622443C Patser: 8.71

Cons/Pat: 0.76

Mouse TTCCAGGCAGHuman CTTCTGGCTGRat ==========Dog ==========

CSLCA 5 20 21 21 0 0C 2 0 0 0 0 0G 9 0 0 0 21 0T 5 0 0 0 0 21

Site: 117633462 Patser: 7.28

Cons/Pat: 2.07

Mouse GAAAGTHuman ======Rat GAAAATDog ======

Site: 117637548C Patser: 7.28

Cons/Pat: 1.94

Mouse GAAAGTHuman ======Rat GAAAGTDog =======

Site: 117633499 Patser: 7.28

Cons/Pat: 1.87

Mouse GAAAGTHuman ======Rat - - - AGTDog ======

CSLHA 0 0 0 0 7 1 24 24C 14 0 0 0 0 0 0 0G 0 24 0 24 15 23 0 0T 10 0 24 0 2 0 0 0

Site: 117636476C Patser: 9.07

Cons/Pat: 0.41

Mouse CGTGAGAAHuman ========Rat GGTGAGAGDog ========

Site: 117622001 Patser: 7.90

Cons/Pat: 0.00

Mouse CGTGTGAAHuman ==========Rat ==========Dog ==========

Site: 117640365C Patser: 7.57

Cons/Pat: 0.01

Mouse TGTGTGAAHuman ========Rat TATGTAAADog ========

CSLLA 10 0 0 7 1 24 10C 2 0 0 0 0 0 2G 10 0 24 15 23 0 10T 2 24 0 2 0 0 2

Site: 117641715 Patser: 7.26

Cons/Pat: 6.33

Mouse GTGGGAAHuman GTGGAAARat GTGGGAADog GTGGGAA

Site: 117641515 Patser: 7.26

Cons/Pat: 3.92

Mouse GTGGGAAHuman GTAGGAARat GTGGGAADog GAAGGAA

Site: 117638263C Patser: 7.26

Cons/Pat: 1.58

Mouse ATGGGAAHuman - - - - - - -Rat ACGGGAADog =======

CMAF01Frequency Matrix:A 8 15 11 12 6 3 1 3 3 2 32 2 6 4 10 10 9 7 14C 5 4 5 7 4 2 2 33 2 1 0 23 2 15 5 3 14 5 7G 14 5 6 3 12 0 34 0 2 33 2 5 16 7 12 14 6 10 9T 10 13 15 15 15 32 0 1 30 1 3 7 13 11 10 10 8 15 7

Sequence Logo:

Site: 117629202 Patser: 8.12

Cons/Pat: 0.02

Mouse ACTTGTGCTGAGGTTTCGCHuman ACTCATGCTAAGATTTTAARat ACTTGTGCTTTGGCTTCAADog ACTCATGCTAAAATCTGAG

Site: 117630786 Patser: 7.54 Cons/Pat: 3.42

Mouse AATGTTGCTGATAAAACTAHuman ===================Rat CATGTTGCTGATAAAACTADog ===================

Site: 117628756 Patser: 6.60 Cons/Pat: -0.02

Mouse CCTTGTGCTGATTAAATAAHuman CCCTTTGCTAGTAAAGTCARat CCTTGTGCTGATTGAATTADog CCCTATGCTAATGAAATCT

RORA1A 10 9 15 9 6 11 21 0 0 0 0 25 7C 2 3 1 1 12 2 0 0 0 0 25 0 5G 7 3 2 0 4 5 4 25 25 0 0 0 2T 6 10 7 15 3 7 0 0 0 25 0 0 10

Site: 117629554 Patser: 11.14

Cons/Pat: 0.00

Mouse AAATAAAGGTCAAHuman =============Rat GAATAAAGGTCAADog ==========TGG

Site: 117625495 Patser: 10.75

Cons/Pat: 0.12

Mouse TTATAAAGGTCAAHuman CTATGAAGATGAARat TTGTAAAGATCAADog =============

Site: 117628611C Patser: 10.75

Cons/Pat: 0.32

Mouse AATTCAAGGTCACHuman =============Rat AATTTAAGGTCACDog =============

AP1

A 0 0 16 5 3 0 16 C 1 0 2 12 0 15 0 G 0 15 0 1 1 3 1 T 17 3 0 0 14 0 1

Site: 117641544 Patser: 8.13

Cons/Pat: 7.69

Mouse TGACTCAHuman TTACTCARat TGACTCADog TTACTCA

Site: 117629136C Patser: 8.13

Cons/Pat: 5.15

Mouse TGACTCAHuman =======Rat TGATTCADog TAATTTA

Site: 117631122C Patser: 8.13

Cons/Pat: 0.62

Mouse TGACTCAHuman =======Rat - - ACTCADog =======

STAT5A1

A 7 18 14 0 0 0 0 10 8 0 33 33 13 2 8C 6 2 4 0 1 32 15 6 0 0 0 0 7 11 8G 8 7 4 0 0 1 6 8 25 33 0 0 4 0 6T 7 3 11 33 32 0 12 9 0 0 0 0 8 19 8

Site: 117625167C Patser: 11.07

Cons/Pat: 1.19

Mouse TAATTCCAGGAAGCCHuman TAATTCCAGTAAA - TRat TAATTCTGAGAAACTDog ===============

Site: 117641763C Patser: 7.96

Cons/Pat: 7.24

Mouse GTCTTCTGAGAAGTAHuman GTCTTCTGAGAACGARat GCCTTCTGAGAAGTADog GTCTTCTGAGAACTA

Site: 117626957C Patser: 7.06

Cons/Pat: 0.00

Mouse AAATTTTAGGAACTAHuman ATGTTTTAAGGACTARat AGGTTTTAGGGACTGDog ===============

NFKappaB1

A 0 0 0 2 11 5 0 0 0 0 1 C 0 0 0 0 1 0 5 13 17 18 15G 18 18 18 16 6 2 2 0 0 0 1 T 0 0 0 0 0 11 11 5 1 0 1

Site: 117634343C Patser: 7.22

Cons/Pat: 0.25

Mouse GGGGCATCCCGHuman GGGA =======Rat ===========Dog ===========

Site: 117624662 Patser: 7.04

Cons/Pat: 0.55

Mouse GTGGGTCCCCCHuman GGGAGACCCACRat GGGAGACCCACDog GGGAGACCCCC

Site: 117634343 Patser: 6.78

Cons/Pat: 0.24

Mouse CGGGATGCCCCHuman ===========Rat =======ACCCDog ===========

RORA2

A 17 15 36 22 2 0 28 0 0 0 0 36 14C 2 0 0 0 12 0 0 0 0 0 36 0 7G 7 4 0 0 13 0 8 36 36 0 0 0 10T 10 17 0 14 9 36 0 0 0 36 0 0 5

Site: 117624871C Patser: 6.63

Cons/Pat: 0.01

Mouse ATCACTGGGTCACHuman ============Rat ATCG - TGGGTCACDog AACATGAAGG - TC

Site: 117629554 Patser: 6.27

Cons/Pat: 0.00

Mouse AAATAAAGGTCAAHuman =============Rat GAATAAAGGTCAADog ==========TGG

Site: 117625495 Patser: 5.88

Cons/Pat: 0.13

Mouse TTATAAAGGTCAAHuman CTATGAAGATGAARat TTGTAAAGATCAADog =============

STAT5A4

A 21 40 18 0 0 5 2 29C 32 15 29 0 0 95 35 21G 31 11 18 0 0 0 6 21T 16 34 35 100 100 0 56 29

Site: 117628243C Patser: 6.09

Cons/Pat: 2.43

Mouse CATTTCTAHuman AGTTTCTARat AGTTTCTADog AGTTTCTA

Site: 117624622 Patser: 6.09

Cons/Pat: 0.04

Mouse CATTTCTTHuman ACTCTCTTRat CGTTTCTCDog ACTCTTGT

Site: 117634806C Patser: 6.09

Cons/Pat: 0.00

Mouse CATTTCTTHuman ========Rat ========Dog ========

STAT5B1

A 9 24 16 0 0 0 0 7 10 0 46 46 17 8 8C 6 2 1 0 0 46 28 11 2 0 0 0 5 10 11G 14 8 3 0 0 0 1 8 34 46 0 0 5 1 7T 11 8 26 46 46 0 17 20 0 0 0 0 19 27 17

Site: 117625167C Patser: 10.00

Cons/Pat: 1.17

Mouse TAATTCCAGGAAGCCHuman TAATTCCAGTAAA – TRat TAATTCTGAGAAACTDog ==============

Site: 117625167 Patser: 9.58

Cons/Pat: 1.16

Mouse GGCTTCCTGGAATTAHuman A -TTTACTGGAATTARat AGTTTCTCAGAATTADog ==============

Site: 117623597 Patser: 7.60

Cons/Pat: 0.02

Mouse ATTTTTCTGGAAATTHuman GTTTT–CTGGACATCRat ATTTT– CAGAACATTDog GTATT -CTGGACGTC