Sequence
atgc intronic sequence ATGC exonic sequence...ttttttttttatcattataggtgatggtgtttagaattttaaaattttaattctttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT
Basic information
species | Glycine max |
transcript | GLYMA06G42210.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G42210.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 3
--ttttttttttatca--------ttataggtg-atggtgtttagaattttaaaattttaattctttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT
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cattctacttctatcaggccatctttatgcatttattttttcttgagctctaagtttcttttttctggagctcta-agttttgtgtattgtccatgttcagGCCTTTCTGGAGCAAAGACTTGAGGAGCTT------GAGACAGTGGAAGATATAAATCATCTAATTTTCACTGATTCTGATATAGCAGTGGTTACTGATCTTGGAC----
upper sequence: GLYMA06G42210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G342254_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------ttttttttttatcatt-ataggtgatggtgtttagaattttaa------aattttaattctttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT
|| || | | || || | | | | | || || | | ||| || | | | || || ||| || |||| | | || | ||| | || || ||| | | || | | | | | | | | ||||| | || |||||||| ||||||||||||||||||||| | || |
gtaagtgtatcggcttcatttagatcattaaattttctgcatatggtctctcaaaattacttatgtgatccatgtattactgctatcatcatctttatgcattattttgaactgtaagagttatatttatgtatcttatcctcatatttagGCATTTCTGGAGCAAAAGCTTGTGGAATTT------GATAGGACGGAGAGGTTGAATCATTTTGTTTTAACTGATTCCGATATAGCAGTGGTTGATGATCTTGGAC----
upper sequence: GLYMA06G42210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G143688_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------ttttttttttatcatt-ataggtgatggtgtttagaattttaa------aattttaattctttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT
|| || | | || || | | | | | || || | | ||| || | | | || || ||| || |||| | | || | ||| | || || ||| | | || | | | | | | | | ||||| | || |||||||| ||||||||||||||||||||| | || |
gtaagtgtatcggcttcatttagatcattaaattttctgcatatgctttctcaaaattacttatgtgatccatgtattactgctatcatcatctttatgcattattttcaactgtaagagttatatttatgtatcttatcctcatatttagGCATTTCTGGAGCAAAAGCTTGTGGAATTT------GATAGGACGGAGAGGTTGAATCATTTTGTTTTAACTGATTCCGATATAGCAGTGGTTGATGATCTTGGAC----
upper sequence: GLYMA06G42210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G350001_T01 (Zea mays), 3'ss of exon 9
---------------------------------------------------------ttttttttttatcattataggtgatggtgtttagaattttaaa----attttaattctttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT
| || | | ||| | || | || | | | |||| ||||| | | | | || || ||| || |||| | | || | ||| | || || ||| | | || | | | | | | | | ||||| | || |||||||| ||||||||||||||||||||| | || |
gtaagtgtatcggcttcatttagatcataaaattttatgcatatgctttctcaaaattacttatgtgatccatgtat-tactgctatcatcatctttatgcattattttcactgtaagagttatatttatgtatcttatcctcatatttagGCATTTCTGGAGCAAAAGCTTGTGGAATTT------GATAGGACGGAGAGGCTGAATCATTTTGTTTTAACTGATTCCGATATAGCAGTGGTTGATGATCTTGGAC----
upper sequence: GLYMA06G42210.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G45320.1 (Arabidopsis thaliana), 3'ss of exon 3
----ttttttttttatca--ttataggtgatggtgtttagaattttaa---aattttaattct--ttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT--
|| ||| ||| | | | |||| || | | | || | ||| | ||| || || | | | | | ||| | ||||||||| | || | | |||| |||| | || | | | | ||| || ||||||||||||||||||||||| |||||||| || | ||| ||
tttattcatttcttagaaagtgtttagtga-agtagctgaattgttgagagaatatgaatgctcattgggtcatgattcttgttaaaatttgtctctgcagACCTTTCTTGAGATGAAGCTCGAGAA--------GAATGAGGGTGGGATAAACCAC----TATATCTTCACTGATTCTGATATAGCTGTGGTTGACGACGTCGGGACTATAT
upper sequence: GLYMA06G42210.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0048g00310.t01 (Vitis vinifera), 3'ss of exon 4
-------ttttttttttatcattatag-gtgatggtgtttagaattttaaaattttaattctttaaacta--aataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT
| | | |||| ||| | || | || | | ||||| | | || | | | | | | || || | | | ||| ||| |||||||||| ||| || | | ||||||| | |||| | |||||||||||||||||| || ||||||||||| |||||||||||||
gaatttatcatcatccagtcatattagagagaaactactttgttatacaaaataatgttaattcacaatgccatttgtttaattgattttctgtgtgcagGTCTTCTTAGAAACAAAGCTTGAGGAGCATTCTCAGGGTCA---TGGGCATATAAATCATTACATCTTCACTGACTCAGATATAGCAGTAGTTGATGATTTAG------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaattctttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT
aaataac putative branch site (score: 2)
ccttttt putative PPT
ttctttaaactaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttttttttatcattataggtgatggtgtttagaattttaaaattttaattctttaaactaaataaccttatgttttccttctttacagacctttttagAAACAAGGCTCCAGAATCTTTCTCAGAAGAAGCCAAAAAATATCACTCATTACATCTTCACTGATTCTGATATAGCAGTGGTTGATGATTTAGGGCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - gatggtg