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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaattaagctgaggacatagtccagtttgtttatatctgaaaaatgaattgtaacataagaacgatttgat...

Basic information

species Zea mays
transcript GRMZM5G801409_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 5'ss of exon 3
CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgt---ccacccccttcttttttattaat-caattaagctga----ggacatagtccagtttgt-ttatatct--gaaaaatgaattgtaacataagaacgatttgat
|| | |||||||| ||| || || ||||| |||||  ||||  | || ||||||||||| ||||| |||||||| |||||||| |||||||| || ||||||||||     | ||  ||   ||||   ||| | |||  | | |    ||| ||||   |   ||| || |  ||  |   ||  |      |||| ||           
CCCAAGGATGACGTCAACAAACCATGCCACCTCACCTCCTTTGTCGGTTACAAGGCTGGAATGACCCACATTGTGCGTGAGGTCGAGAAGCCTGGTTCCAgtatgtgtctaatccttttgccttttgccaatgctattttgttcaacctggaaatagatgaccatgtattgtgactatgcggaagaagcaactacattag-----------

upper sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G36780.1 (Glycine max), 5'ss of exon 3
CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgt-ccacccccttcttttttattaa--tcaattaagctgaggacatagtccagtttgtttatatctgaaaaatgaattg--taacataagaacgatttgat
|| | ||||||| |    ||| |   | | |||||||| ||| | || |||||||| || ||||||||||||||  | ||||| |||||||||||||| |||  || |||  |  | ||  || ||| |  | || | |  | | | | |   ||| | ||||| ||       | | | |||   | ||  || | || |    
CCCAAGGATGACCCATCCAAGGCACCCAAGCTCACTGCATTCTTGGGTTACAAGGCCGGTATGACTCACATTGTTAGAGAGGTCGAGAAGCCAGGATCAAgtgagttccatactttgctaattaattgaagttaaatgatataatgtcgtcaacca-tgtgttt-tactcagctacttacttgatcaccaatagcaggactg---

upper sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G30810.1 (Glycine max), 5'ss of exon 3
CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaa---ttaagctgaggacatagtccagtttgtttatatctgaaaaatgaattgtaacataagaacgatttgat
|| | ||||||| |    ||| |   | | |||||||| ||| | || ||||||||||| ||||||||||||||  | ||||| |||||||||||||| |||  |   | ||  | || ||||  ||||  |   | | |   |  |    ||| |   ||| | |  ||      | | |||  |   |  | ||      |
CCCAAGGATGACCCATCCAAGGCACCCAAGCTCACTGCATTCTTGGGTTACAAGGCTGGTATGACTCACATTGTTAGAGAGGTCGAGAAGCCAGGATCAAgtgag---aaccattactcttttgctaattgaagttgatgtatataatgctgtcaaccatgtgttttactatcttcttatttgataatcagtagcgggactgt

upper sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G00280.1 (Glycine max), 5'ss of exon 3
CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaattaagctgaggacatagtccagtttgtttatatctgaaaaatgaattgtaacataagaacgatttgat---
|| |  ||  |  | |   | || |||    | ||||| ||  | |||||||||||||| ||||| ||||||||  | ||||||||||| || ||||| |||| ||    |   || ||  || | |||   |     || ||  |  ||    ||| ||  | |   |     | ||||||| |  || |       ||   
CCAAAAGACAATCCTAGTCAACCATGCGGGTTGACTGCTTTTGTGGGCTACAAGGCTGGAATGACCCACATTGTTAGAGAGGTTGAGAAACCTGGATCAAgtaagtgtgacttttttttaattttaaat---tctgaatgtgggaagggtaatattttttattgttaaactgtagcattgtaaaaccagtatttacaaatgta

upper sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 2
lower sequence: PP1S330_36V6.3 (Physcomitrella patens), 5'ss of exon 1
-------------------CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccaccc---------------ccttcttttttattaatcaattaagc--tgaggacatagtccagtttgtttatatctgaaaa----atgaattgtaaca--taagaacgatttgat--------------------
                   || | ||||||  ||   |||     |||  | ||  | ||||||||||||||||| ||||||||||||||||| || ||||| || ||||| |||||||   ||  ||                  || ||    |  |  |      |  |      | | |||    | | | ||| |||   |        |  |||       | |  ||| | ||                      
CGGGAAGGTGAAGACCTTTCCCAAGGATGATCCCGTCAAGAAGCCCCACTTGACCTCTTTCCTTGGCTACAAGGCCGGCATGACTCACATTGTTCGCGAGgtggaaaagcccggatccaagctgcacaagaaggagacatgcgaggccgtcaccatcgtcgagacgccacccatcatcgtcgtagggttggtggcttacatcaagactcctcgcgggttgaggtcgttgaacacggtgtgggctcagcacctgagcgacgag

upper sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 2
lower sequence: EFJ30452 (Selaginella moellendorffii), 5'ss of exon 2
CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaattaagctgaggacatagtccagtttgtttatatctgaaaaatgaattgtaacataagaacgatttgat
||| |||||||  | | ||||     |||| | || |||||| | || |||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||| |||| |     |  ||   |||  || |   |||| |       || || ||||   |                                      
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctg---ttcttcccatt--tcga--gagctaaatttcgcgttca-tttgcccag-------------------------------------

upper sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 2
lower sequence: EFJ23085 (Selaginella moellendorffii), 5'ss of exon 2
CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaattaagctgaggacatagtccagtttgtttatatctgaaaaatgaattgtaacataagaacgatttgat
||| |||||||  | | ||||     |||| | || |||||| | || |||||||| || |||||||| || ||||| ||||| |||||||||||||| |||| |||| |     |  ||   |||  || |   |||| |       || || |||||  |                                      
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGTATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctg---ttcttcccatt--tcga--gagctaaatttcgcgttca-tttgtccag-------------------------------------

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|211158271|gb|FL403878.1|FL403878
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211133812|gb|FL389470.1|FL389470
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGA-GTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211286183|gb|FL403232.1|FL403232
EST:     CAA-GCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211223980|gb|FL295886.1|FL295886
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCC-TC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211226042|gb|FL295896.1|FL295896
EST:     CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
genomic: CAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAACCCCTC
EST: gi|211223978|gb|FL295884.1|FL295884
EST:     AAGGCTGGCATGACTCACATTGTCCGTGAGGCTTGAGAAGC-AGGATCCA                         AACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAAC
genomic: AAGGCTGGCATGACTCACATTGTCCGTGAGG-TTGAGAAGCCAGGATCCAgtatgtccac ... atttctacagAACTCCATAAGAAGGAAACTTGTGAGGCTGTTACCATCATTGAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaattaagctgaggacatagtccagtttgtttatatctgaaaaatgaattgtaacataagaacgatttgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC