Sequence
atgc intronic sequence ATGC exonic sequence...cgagttaggtcaaatccacattctaaaatgatagtaattaacttcacttgtgtacataatttgtttgtttttgactcgtttcttgtattttgggtttcagATCATCAAGAACCACCTTGAGCCATTAACAGATCAGCAGTTGATGGGAATTTGTAATCTACAACAGTCTTCCCAGCAGGCTGAGGATGCTTTAAATCAAG
Basic information
species | Glycine max |
transcript | GLYMA02G10820.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G10820.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g03230.t01 (Vitis vinifera), 3'ss of exon 9
-------cgagttaggtcaaatccacattctaaaatgatagtaattaacttcactt---------gtgtacataatttgtttgttt--------ttgactcgtttcttgtattttgggtttcagATCATCAAGAACCACCTTGAGCCATTAACAGATCAGCAGTTGATGGGAATTTGTAATCTACAACAGTCTTCCCAGCAGGCTGAGGATGCTTTAAATCAAG
|| | | | | | | || | || | | | | | ||| ||| |||| || | | | | | || | ||| | ||||||||| | |||||| ||||| || ||||||||||||||| ||||||| || ||||||||||||||||| || ||||| ||||||||||| ||| ||||
gtaatttgaagatttattgcttttagaccttgaatcttttttatccagttctgcaatggctgaaggaatgtatagtttttttggttgattcacatctatttctattttatttttggagtttcagATACTTGGGAACCAACTTGAACCTTTAACAGATCAGCAGCTGATGGGCATATGTAATCTACAACAGTCCTCACAGCAAGCTGAGGATGCATTATCACAAG
upper sequence: GLYMA02G10820.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ29724 (Selaginella moellendorffii), 3'ss of exon 6
cgagttaggtcaaatccacattctaaaatgatagtaattaacttcacttgtgtacataatttgtttgtttttgactcgtttcttgtattttgggtttcagATCATCAAGAACCACCTTGAGCCATTAACAGATCAGCAGTTGATGGGAATTTGTAATCTACAACAGTCTTCCCAGCAGGCTGAGGATGCTTTAAATCAAG
| | | | ||| | | | ||| || | || || || | | | ||||| | | || ||||| || | ||||| |||||| | ||||| |||||||||||||||||||| || |||||||| ||||||||| | || |
------------------------------gtgctgctgtgtctttcttttcctcgt--ttttttcgaaagtg-cttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG
upper sequence: GLYMA02G10820.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ28227 (Selaginella moellendorffii), 3'ss of exon 6
cgagttaggtcaaatccacattctaaaatgatagtaattaacttcacttgtgtacataatttgtttgtttttgactcgtttcttgtattttgggtttcagATCATCAAGAACCACCTTGAGCCATTAACAGATCAGCAGTTGATGGGAATTTGTAATCTACAACAGTCTTCCCAGCAGGCTGAGGATGCTTTAAATCAAG
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------------------------------gtgctgctgtgtctttcttttcctcgt--tttttccgaaagtg-cttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgtgtacataatttgtttgtttttgactcgtttcttgtattttgggtttcagATCATCAAGAACCACCTTGAGCCATTAACAGATCAGCAGTTGATGGGAATTTGTAATCTACAACAGTCTTCCCAGCAGGCTGAGGATGCTTTAAATCAAG
ttttgac putative branch site (score: 3)
ataatttgtttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgagttaggtcaaatccacattctaaaatgatagtaattaacttcacttgtgtacataatttgtttgtttttgactcgtttcttgtattttgggtttcagATCATCAAGAACCACCTTGAGCCATTAACAGATCAGCAGTTGATGGGAATTTGTAATCTACAACAGTCTTCCCAGCAGGCTGAGGATGCTTTAAATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - cacattc
- - - - - - - - - - - - - - - - - - - - acttcac
- - - - - - - - - - - - - - - - - - - - - - - - tgtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt