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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttttatgaaatcactgtaatagttctttccacagtttggctttgcctaacttgattttgttgaaccttggacctggacaatggaag

Basic information

species Zea mays
transcript GRMZM2G170595_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g47940.1 (Oryza sativa), 5'ss of exon 7
CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttttatgaaatcactgtaa-tag---ttctttccacagtttggctttgcctaactt---gattttgttgaaccttggacctggacaatggaag
||| ||||||||||| ||| |||| ||||||||||||||||||||||| || |||||||||||||| ||||| || || ||||| || |||||| | |||||||    | |   ||   |   ||| ||    ||  ||    | |||||| |   |||||||   | || |||||||| ||  |       |       
CATAATCGAGTATTTATGGAGGGCTAAGCAGCCCTATAATGTTTCTGTAGCAGCAGAAGTTTCAGCCTGTGCTGCCTTGCAGAACCCGACTTATTTAGAGgtatgtgctctggaaacatatcataaataaatttttgtttagtaatttggcatctgctaactttgtgcttctgttgaacatttcattactgaag------

upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 8
CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttttatgaaatcac-tgtaatagttctttcc--acagtttggctttgcctaacttgattttgttgaaccttggacctggacaatggaag----
 || || |||||| | ||| | || |||||||| |||||||| ||||| || || ||| |||| ||||||||||| || || ||||| || ||||| ||||| |  ||||| |    |  | | ||| |  | | |    |  | ||  |      ||  ||    || |||||  |||      ||   ||  |     
TATAATTGAGTATCTTTGGAGAGCAAAGCAGCCGTATAATGTATCTGTTGCTGCTGAAATTTCTGCATGTGCAGCATTGCAAAATCCTACCTATCTAGAGgtttttcttttgttcttttgcatataacacatgtatgttaattgattatcccctagtacattatggttattgaaagttgttgtaagagtttgatataaca

upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv18s0072g00940.t01 (Vitis vinifera), 5'ss of exon 8
CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttttatgaaatcactgtaatagttctttccacagtttggctttgcctaacttgattttgttgaaccttggacctggacaatggaag------------
|||||| |||||| | ||| | || ||||| || |||||||||||||| || || |||||||| ||||||||||| || ||||||||  | ||| ||||||||    |||| |   ||    ||| || || ||     | | ||| |||  |   ||||  ||| | | |||    |  |  | ||| |  |            
CATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGAAGTTTCTGCATGTGCAGCATTGCAGAATCCCGCCTATTTGGAGgtactttttttcttttattttagtatta-tttttgttgta-tctggttttatcc--cttgcatttataggaccaaacatttcaa-aataggggataatgagtatc

upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S175_129V6.1 (Physcomitrella patens), 5'ss of exon 8
CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttttatgaaatca----ctgtaatagttctttcca-cagtttggctt-----tgcctaact-tgattttgttgaaccttggacctggacaatggaag-----------------------------------------------------------------------------
  | || ||||| |||||||| |||||||||||||| ||||| ||||| || || |||||  | |||||||||||| |    |||||||  ||  ||||||||         | || | |       ||||| |    || | ||||||    |     || |||| | || |  | | |    |  |   || ||| |  |                                                                               
TCTGATTGAGTACTTGTGGCGAGCCAAGCAGCCCTACAATGTCTCTGTTGCTGCTGAAGTGGCTGCATGTGCAGCTCTTACTAATCCAAAATACTTGGAGgtaatggcgacttaaagttaaacctcataatattcaaatctagcagtttattctgatagtgtctaagtctgctgctatcggcaataagttttgtacagtttaccacctatttagagatgtacctaaaattaataccggttgcattttctcttgtcctcaatagctcatgcttgtataacag

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|71332193|gb|DR803017.1|DR803017
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|26457570|gb|CA829153.1|CA829153
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|21987125|gb|BQ778653.1|BQ778653
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|22543121|gb|BU093559.1|BU093559
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|211376337|gb|FL031210.1|FL031210
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|32931414|gb|CF036226.1|CF036226
EST:     GTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTGCTGGTAAAAGAAAGGGGGAGGTTGTTTAATCTTCTC
genomic: GTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|21760175|gb|BQ635716.1|BQ635716
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|22473177|gb|BU037657.1|BU037657
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|211376338|gb|FL031211.1|FL031211
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|5847509|gb|AW000588.1|AW000588
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|22542058|gb|BU092496.1|BU092496
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTC
EST: gi|6227157|gb|AW155686.1|AW155686
EST:     CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAG                         AATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTTGTT-AATCTTCT
genomic: CCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTT-GTTTAATCTTCT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 107

CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 86

CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttt ... acaatggaagAATGTGAAAAATTTACTGGTAAAAGAAAGGGAGAGGTTGTTTAATCTTCTCAAGGGAATACCATTCCTGAAGCCATTTCCCAGTCATTCTAACTTCATTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGAAGTTTCAGCATGTGCAGCTTTACAGAATCCAACTTATCTGGAGgtatcacttttatgaaatcactgtaatagttctttccacagtttggctttgcctaacttgattttgttgaaccttggacctggacaatggaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT