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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGGTTTTTATGAGAACTTTGACTCTGATTTTATTGGGATTAGAACAAAAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaatgcagtttgtgccacattgttctttcttgttttacatgtttctggtcagaaatgctcatatttttatatgttttttgtttatttatatttgtttcagcttttgtgaattccgtcgaatttatcttaactaacgtttttccatctggccattcctgtctaacctttctgggttacag

Basic information

species Physcomitrella patens
transcript PP1S44_102V6.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 15
TGAAGGTTTTTATGAGAACTTTGACTCTGATTTTATTGGGATTAGAACAAAAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaatgcagtttgtgccacattgttctttcttgttttacatgtttctggtcagaaatgctcatatttttatatgttttttgtttatttatatttgtttcagcttttgtgaattccgtcgaatttatcttaactaacgtttttccatctggccattcctgtctaacctttctgggttacag
|||       |||||||     ||  | ||||| ||||  ||||||||||| ||  | |||||||||||| | |||||||| ||||||||||| |||||||||       ||    |||||  | |||     | || |  || || | |   |||  ||  || || ||||    |    ||||    || |    | |   ||                                                                                 
TGAGCCGCACTATGAGAGGGAAGATCCAGATTTCATTGATATTAGAACAAAGGCACGTGAGGTGTTGCAGAGGGAAGATGATTTAAATGAAATAGTGCAGgtactattt-tgagccttgtga-atatttactctcctggaattccacgat---ggtttgacctg-tcttattgaagttaccttttctcatactgtcgtatccctcc--------------------------------------------------------------------------------

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 12
TGAAGGTTTTTATGAGAACTTTGACTCTGATTTTATTGGGATTAGAACAAAAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaatgcagtttgtgccacattgttctttcttgttttacatgtttctggt-cagaaatgctcatatttttatatgttttttgtttatttatatttgtttcagcttttgtgaattccgtcgaatttatcttaactaacgtttttccatctggccattcctgtctaacctttctgggttacag
|||    ||||||||||| |||||  | ||||| ||||  ||||| ||||||||  | |||||||||||| | || || ||  |||||||||||||||||||| |          ||||   | |||  |  ||||    ||||| ||       | |    ||| |   | |||| |   || ||   |    |     |||||   | |    | ||||    |||   || || |  ||      |||||   | | |   |||   || |   || ||| |||
TGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtagga---------tttg---ctcatcatcttttcca--tttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggcattggcatgttttgtcatgca-gcattcaaatgaaa--atttttatcaatagcactccatt--gtcttgattgt--gacttccgtgtgtt-cag

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
TGAAGGTTTTTATGAGAACTTTGACTCTGATTTTATTGGGATTAGAACAAAAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaatgcagtttgtgccacattgttctttcttgttttacatgtttctg-gtcagaaatgctcatatttttatatgttttttgtttatttatatttgtttcagcttttgtgaattccgtcgaatttatcttaactaacgtttttccatctggccattcctgtctaacctttctgggttacag
 |||  |||||||||| | | |||  | ||||||||    || || ||||| ||| | |||||| ||||  ||||||||||| |||||||||||||||| |||       ||   |       |  || |  |||  | ||  |||  |   || |  |||||||  |   ||   ||| || ||        | ||| |||                                                                                     
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgta-------tgttttcctccttagcttttatttttctattacacagctagatgagatagaaatgagccatttcccata-gtgttccaagacatgatacttgggagga-------------------------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37836831|gb|BJ594839.1|BJ594839
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37838710|gb|BJ596718.1|BJ596718
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|162276207|gb|FC452899.1|FC452899
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37845049|gb|BJ603057.1|BJ603057
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37838267|gb|BJ596275.1|BJ596275
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|22131932|gb|BQ826891.1|BQ826891
EST:     CAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: CAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37852823|gb|BJ610831.1|BJ610831
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|15327219|gb|BI487765.1|BI487765
EST:     AATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTNGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37848114|gb|BJ606122.1|BJ606122
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|162276206|gb|FC452898.1|FC452898
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|67578993|gb|BJ951144.1|BJ951144
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37834888|gb|BJ592900.1|BJ592900
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|162186096|gb|FC361300.1|FC361300
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37846602|gb|BJ604610.1|BJ604610
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|162258844|gb|FC434851.1|FC434851
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37853133|gb|BJ611141.1|BJ611141
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37822114|gb|BJ580180.1|BJ580180
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37834988|gb|BJ593000.1|BJ593000
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|162239653|gb|FC418014.1|FC418014
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37848974|gb|BJ606982.1|BJ606982
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|37850336|gb|BJ608344.1|BJ608344
EST:     AGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATG-AAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
EST: gi|162179502|gb|FC356542.1|FC356542
EST:     AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAG                         CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT
genomic: AAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 13

TGAAGGTTTTTATGAGAACTTTGACTCTGATTTTATTGGGATTAGAACAAAAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaa ... tgggttacagCTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGGTTTTTATGAGAACTTTGACTCTGATTTTATTGGGATTAGAACAAAAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaatgcagtttgtgccacattgttctttcttgttttacatgtttctggtcagaaatgctcatatttttatatgttttttgtttatttatatttgtttcagcttttgtgaattccgtcgaatttatcttaactaacgtttttccatctggccattcctgtctaacctttctgggttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG