Sequence
atgc intronic sequence ATGC exonic sequence...atatacattagtttctttgagtcaataccaagtcagaatggtccttctggtattgctaaactttgtgttttatatgaatctaataaatattatgaaatagGAGCCAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
Basic information
species | Glycine max |
transcript | GLYMA04G09780.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G019153_T01 (Zea mays), 3'ss of exon 9
--------------------atatacattagtttctttgagtcaataccaagtcagaatggtccttctggtattgctaaactttgtgttt-tatatgaatctaataaatattatgaaatagGAGCCAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
| | | | || | || | |||| | | | | | || || |||| | | | | ||||| | | |||| || | || ||| | || ||||||| ||||| |||||||| || |||||||| || ||| | |||||| ||| |||||||||||| |
gtgagtttttcttttcttttaattgctacaattgcatttaagtaatattc--taaatttctaattccctatactgtataactgtctatgtatatataatcatgttaaa-ataacttaacagGTGTCAGAGTAGAAGGGATCTTACGACAAGCTGCAGATGTTGAAGATGTTAAGCGTCGAATTCAGGAATATGAACAGG
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G24580.1 (Arabidopsis thaliana), 3'ss of exon 8
atatacattagtttctttgagtcaataccaagtcagaatggtccttctggtattgctaaactttgtgttttatatgaatctaataaatattatgaaat-----agGAGCCAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
| | | | || || | ||||| | |||| ||| | | | || ||||| | | |||| ||||| || ||||||||||||||| ||||||| |||||||||||||| ||||||| ||| |||| |||||||| |||
------------------gtattagtttcaggttttttcag--cttcttttgctgctttgttttac---tcactctgagctgataaagacaacaaaatcttgcagGAGTCAGGATAGAAGGAATCTTGAGACAAGCTGCTGATGTTGATGATGTTGAACACCGAATTCGCGAATATGAGAAAG
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g07310.t01 (Vitis vinifera), 3'ss of exon 7
atatacattagtttctttgagtcaataccaagtcagaatggtccttctggtattgctaaactttgtgttttatatgaatctaataaat---attatgaaatagGAGCCAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
| ||| | ||| | | | || | | | | | | | | ||||| | ||||| | || | | | || | ||||| ||| |||||||| |||||||||||||| || ||||| ||||| |||||| ||||| |||||||||||||| |||
--tcaaattgatgcaactgaaagtctctttctttaatggtgtagtcattgacatatttatttgtttgtttggt-tgaatatgattatttgagtaatttgacagGAGTCAAAATAGAAGGGATCTTGCGACAAGCTGCAGATGTCGATGATGTTGAATGTCGAATTCGGGAATATGAAAAAG
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 7
-----atatacattagtttctttgagtcaataccaagtcagaatggtccttctggtattgctaa-actttgtgttttata--tgaat----ctaata--aatattatga--------aatagGAGCCAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
| || | | ||| | | || ||| | | ||| ||| |||| | | || || | | ||||| ||||| | | | | | || ||| | | | ||||||||||||||||| | || |||||||| || |||||||| || || || |||||||||||||
gtatgacatccctccgttgagcatacttaaatgcaatccgcataggtgtatctattattccaattgctgtggaagtcacgattgaatggcactaattttagtgtctttattcgtatcaacagGCGTTGGCGTCGAAGGAATCTTGCGACAGTCCGCAGATGTTGAAGATGTTGAACGGCGTGTGCGTGAATATGAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctggtattgctaaactttgtgttttatatgaatctaataaatattatgaaatagGAGCCAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
tttgtgttttatatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatacattagtttctttgagtcaataccaagtcagaatggtccttctggtattgctaaactttgtgttttatatgaatctaataaatattatgaaatagGAGCCAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - caagtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - gctaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgt