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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactttcatcatgttaatttcatcatttcttctcctctgactgtaatgaagcttattatcccaatgtgatgtaaatgcctaatcacttttgtatg...

Basic information

species Zea mays
transcript GRMZM2G156800_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156800_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g55560.2 (Oryza sativa), 5'ss of exon 7
TTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatga--actt--tcatcatgttaatttcatcatttcttctcctctgactgtaatgaagcttattatcccaatgtgatgtaaatgcctaatcacttttgtatg
||||||||||||||||||||||||||| |||||||||| |||||||||||||||||||||||  ||   |||  || |||| | ||||||||  | | || |    |   | | || ||   ||  |  | | | ||    || | |||      |||  | | 
TTGAGTACTGCAGCTCCTAATCTTTCACTGAAGGGAACTCCATACTGGATGGCTCCTGAGgtgagactgcttgttcttcatataaatttcatggtgtattttttattagatttcataaa--ctacaa--ctattatgtcaaaactccctctgttttttgatgta

upper sequence: GRMZM2G156800_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA05G10050.1 (Glycine max), 5'ss of exon 6
TTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactttcatcatgttaatttcatcatttct-tctcctctgactgtaatgaagcttattatcccaatgtgatgtaaatgcctaatcacttttgtatg
 | | |      |   |||||||||| |||| |||||  ||||||||||||||||| |||||||    || |   |  |||   |  | || ||| ||||         | |  ||   |   || |  ||                              
CTTACTGGGTTTGAAGCTAATCTTTCTTTGAGGGGAAGTCCATACTGGATGGCTCCAGAGgtatagttttactctacattaccct-gtaatgtctgtctcgcacattcctcactaacacttcgattctcatacag--------------------------

upper sequence: GRMZM2G156800_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA04G03870.3 (Glycine max), 5'ss of exon 9
TTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactttcatcatgttaatttcatcatttcttctcctctgactgtaatgaag--cttattatcccaatgtgatgtaaatgcctaatcacttttgtatg
 |||       | |   | | ||||||||||||||||  || |||||||||||||||||||||      ||  |  | |||  |      |||    |         ||||||| |  |   || |   | ||| || |        ||             
CTGACAGAGAAATCATATGAACTTTCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAGgta-atttattagttgtattatctatggagttttagatggggaatgagtaatgacgtgcccctttttttactgtaatttgttgattgaag------------

upper sequence: GRMZM2G156800_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G06200.1 (Glycine max), 5'ss of exon 10
TTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaact-------ttcatcatgtta--atttcatcatttcttctcctctgactgtaatgaagcttattatcccaatgtgatgtaaatgcctaatcacttttgtatg
 | | |      | | |  ||||||| ||||||||||  ||||| ||||||||||| |||||||  |||       || || |   ||  | | ||  || |||  | |  |  || ||  ||  ||||||   |  |  ||  |                        
CTAACTGGACATGTTGCAGATCTTTCTTTGAAGGGAAGTCCATATTGGATGGCTCCAGAGgtatatactaattaagtttataactctattactccacgatgtctcatgcgttctctata--gacacttattcctcatacatgcag------------------------

upper sequence: GRMZM2G156800_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA06G03970.1 (Glycine max), 5'ss of exon 8
TTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactttcatcatgttaatttcatcatttcttctcctctgactgtaatgaag----cttattatcccaatgtgatgtaaatgcctaatcacttttgtatg
 |||       | |   | | || |||||||||||||  || |||||||||||||||||||||      ||  |  | |||  |      |||    |         ||||||  |    | | || |   | ||| || |   |    ||             
CTGACAGAGAAATCATATGAACTATCATTGAAGGGAAGTCCCTACTGGATGGCTCCTGAGgta-atttatttgttgtattatctatggagttttagatgggtaatgagtaatgccgtgcccctttttttttactgtaatttgtttattgaag------------

upper sequence: GRMZM2G156800_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA17G20460.1 (Glycine max), 5'ss of exon 8
TTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactttcatcatgttaatttcatcatttcttctcctctgactgtaatgaagcttattatcccaatgtgatgtaaatgcctaatcacttttgtatg
 | | |      |   |||||||||| |||| |||||  ||||||||||||||||| |||||||   ||| |   |  |||   |      | | ||||         | |  ||       || |  ||                              
CTAACTGGGTTTGAAGCTAATCTTTCTTTGAGGGGAAGTCCATACTGGATGGCTCCAGAGgtatattcttactctacattaccctgtaatgtccatctcacacattcctcactaacacctcaattctcatacag--------------------------

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|87156020|gb|DY400809.1|DY400809
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|22542085|gb|BU092523.1|BU092523
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|60345120|gb|DN212093.1|DN212093
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|22473422|gb|BU037902.1|BU037902
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|50338068|gb|CO533194.1|CO533194
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|87157200|gb|DY401989.1|DY401989
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|26558715|gb|CA830950.1|CA830950
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|6031429|gb|AW076331.1|AW076331
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|211321744|gb|FL182473.1|FL182473
EST:     CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: CAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
EST: gi|211321747|gb|FL182476.1|FL182476
EST:     AGCTCCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAG                         GTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT
genomic: AGCT-CCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactt ... tatgttacagGTTGTTCGGGCTACACTCGATAAAAGTGCAGGTTATGATCTTGCTGTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAGTACTGCAGCTCCTAATCTTTCATTGAAGGGAACACCATACTGGATGGCTCCTGAGgtatgaactttcatcatgttaatttcatcatttcttctcctctgactgtaatgaagcttattatcccaatgtgatgtaaatgcctaatcacttttgtatg

- - - - - CAGCTC
- - - - - - - - - - - - -  TTGAAG