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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgttgtatggctggttattgcttgaactgggtggtggagggctgatttgcacctttttcattgtgtaactttattgactatgtcacttctttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGATATAGCTTCTCCAAAAGTGACGAAGAGCTACTCACACCTGAGGTTGACAC

Basic information

species Glycine max
transcript GLYMA12G04460.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 10
gtaagatgt---tgtatggctgg---------ttattgcttgaactgggtggtggagg-gctgatttgcacctttttcattgtgtaactttattgactatgtcacttctttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGATATAGCTTCTCCAAAAGTGACGAAGAGCTACTCACACCTGAGGTTGACAC
||||||  |   |   |||   |         |||||  ||    |   |  |  |     | ||||        || ||  ||| || || |  | | ||| |     ||   |||| | ||||| ||||| ||||||||||| |||||||| || |||||||||||||| ||||| |||||| |||| ||||| || ||||| ||| ||||||| |
gtaagacctccttacttggacagaaccaggttttattttttattttatttaatttatttatttatttattttcaattaatattgtcacattctctattttgttatcatctttaagcagATGAAAGGTAGTGATACATCCACAGCAGAATCAGGATCTGAAGCTGAAGATATTGCTTCCCCAAAAATGACTAAGAGTTATTCACAACTGCGGTTGACTC
















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|7924506|gb|AW830532.1|AW830532
EST:     TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATG                         GTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT
genomic: TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATGgtaagatgtt ... tttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT
EST: gi|19053078|gb|BM731745.1|BM731745
EST:     TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATG                         GTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT
genomic: TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATGgtaagatgtt ... tttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT
EST: gi|22524635|gb|BU083446.1|BU083446
EST:     TAAATAGTGAAGGAAAGGTTATTGCCTATGCCAGACCACAATATCCAATG                         GTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCGGAAGCTGAAGAT
genomic: TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATGgtaagatgtt ... tttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT
EST: gi|208268732|gb|GE069433.1|GE069433
EST:     TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATG                         GTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT
genomic: TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATGgtaagatgtt ... tttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT
EST: gi|193359037|gb|FK325467.1|FK325467
EST:     GCCAGACCACAATTATCCAATG                         GTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGA
genomic: GCCAGACCACAA-TATCCAATGgtaagatgtt ... tttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGA
EST: gi|193725887|gb|FK660195.1|FK660195
EST:     TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATG                         GTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT
genomic: TAAACAGTGAAGGGAAGGTTATTGCCTATGCCAGACCACAATATCCAATGgtaagatgtt ... tttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgcacctttttcattgtgtaactttattgactatgtcacttctttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGATATAGCTTCTCCAAAAGTGACGAAGAGCTACTCACACCTGAGGTTGACAC
                           tattgac  putative branch site (score: 2)
                                    tgtcacttctttctt  putative PPT
                     taactttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgttgtatggctggttattgcttgaactgggtggtggagggctgatttgcacctttttcattgtgtaactttattgactatgtcacttctttcttgcagGTAAAAGGCAGTGACACATCCACAGCTGAATCAGGGTCAGAAGCTGAAGATATAGCTTCTCCAAAAGTGACGAAGAGCTACTCACACCTGAGGTTGACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT