Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaaagcagtatattcctttcatgcatattttctgttgacatgattacaagattaatctttcattttaatttcctagACTACTGGTATGGATCCAATAATAAGAAGGCATGTGTGGGACATAATTGAAAATGCAAAGAGAGGGCGTGCCATTGTTCTTACAACACACTCTATGGAAG
Basic information
species | Glycine max |
transcript | GLYMA04G34140.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G34140.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os08g30740.1 (Oryza sativa), 3'ss of exon 12
gtatgcaaagcagtatattcctttcatgcatattttctgttgaca-tgattacaagattaatctttcattttaatttcc---tagACTACTGGTATGGATCCAATAATAAGAAGGCATGTGTGGGACATAATTGAAAATGCAAAGAGAGGGCGTGCCATTGTTCTTACAACACACTCTATGGAAG
| | | | | ||| | || | | || | | | || | | | |||| || | || | | |||||||||| ||||||||||||| ||| |||||||| |||||||| || || | ||||||| ||| | || ||||| | || || || || ||||| |
--gtaaagaccgccaaatttgctacaaacttccttccaaacatcccttatcatgtg-ctgatctaacaatgtatatcctacacagACTACTGGCATGGATCCAATAACAAGGAGGCATGTCTGGGACATCATAGAGGAAGCAAAGAAAGGAAGAGCTATTGTCTTGACCACCCATTCCATGGAGG
upper sequence: GLYMA04G34140.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G142249_T01 (Zea mays), 3'ss of exon 12
------gtatgcaaagcagtatattcctttcatgcat--attttctgttgacatgattacaagattaatct--ttcatttta---atttcctagACTACTGGTATGGATCCAATAATAAGAAGGCATGTGTGGGACATAATTGAAAATGCAAAGAGAGGGCGTGCCATTGTTCTTACAACACACTCTATGGAAG
|| ||| | | ||| ||| | | | | | || || | | ||| || ||||| | | | || || ||||||||||| ||||||||||||| ||| |||||||| |||||||| || || | || |||| ||| | || ||||| | || || || || ||||| |
gtgaggaaatagaaaaaatttcattgttttgttccttagactcccttgtggccctgtcacat-atcaatctaactaaatgtatatgctttgtagACTACTGGCATGGATCCAATAACAAGGAGGCATGTCTGGGACATCATAGAGGAGGCCAAGAAAGGAAGAGCTATTGTCTTGACCACCCATTCCATGGAGG
upper sequence: GLYMA04G34140.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv17s0000g05850.t01 (Vitis vinifera), 3'ss of exon 12
gtatgcaaagcagtatattcctttcatgcatattttctgttgacatgattacaagattaatctttcattttaatttcctagACTACTGGTATGGATCCAATAATAAGAAGGCATGTGTGGGACATAATTGAAAATGCAAAGAGAGGGCGTGCCATTGTTCTTACAACACACTCTATGGAAG
||||||| | || | | | || | || || || | | || || || |||| |||| ||||| ||||| ||||| || |||| || |||||||||||||||||||| || |||||||||| ||| ||||||||||| || || |||||||| |||||||
gtatgcagactag-agacttctcctttctgcatgtttctttaatgtatttgtttcatacgaggtttcttttgatttg-tagACAACTGGCATGGACCCGATAACGAGGAGGCATGTGTGGGACATAATAGAGAATGCAAAGAAAGGACGTGCCATTGTCCTAACTACACACTCAATGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatattttctgttgacatgattacaagattaatctttcattttaatttcctagACTACTGGTATGGATCCAATAATAAGAAGGCATGTGTGGGACATAATTGAAAATGCAAAGAGAGGGCGTGCCATTGTTCTTACAACACACTCTATGGAAG
ttttaat putative branch site (score: 3)
tttcct CT-rich tract
attacaagattaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaaagcagtatattcctttcatgcatattttctgttgacatgattacaagattaatctttcattttaatttcctagACTACTGGTATGGATCCAATAATAAGAAGGCATGTGTGGGACATAATTGAAAATGCAAAGAGAGGGCGTGCCATTGTTCTTACAACACACTCTATGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG