Sequence
atgc intronic sequence ATGC exonic sequence...tgtgttgagtcgttgactattaaagtcagtcaaagctgtatattgttgaacgtgtgttatttttgtgtgtacatgtgacttaaaatatgtaattattcagGTTGGATTGGCCATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCAGAAGACCCCTTATTGATTCAGAGATGGGATGCTGAATTTT
Basic information
species | Glycine max |
transcript | GLYMA10G42290.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G42290.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G801651_T01 (Zea mays), 3'ss of exon 1
-----------------------------tgtgttgagtcgttgactatt--aaagtca-gtcaaagctgtatattgttgaacgtgtgttatttttgtgtgtac-atgtgacttaaaatatgt--aattattcagGTTGGATTGGCCATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCAGAAGACCCCTTATTGATTCAGAGATGGGATGCTGAATTTT
|| ||| | | | ||| | ||| ||| | | | || | || || || | || || | | || | | || |||| | ||||||||| | | | || || |||||||||||||||||||| ||||| || |||||||| || || ||| | |||||||||||||||||| | |||||||
gtaagtgccaatatctcgatatgaatttgcatgactagtaactaaggaaaggaaaaccgtgtccaagttttct-ttctcataca-gtacaatctctgctagttctgtcaagattgacgtctgctcaattttgcagGTTGGACTAACTGTTGTGGTTGTGGAAAGTGCTGTTACATCAATATACATATGCTATGCCGAGGATCCCCTTTTGATTCAGAGATGGGATCCCGAATTTT
upper sequence: GLYMA10G42290.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G25500.2 (Arabidopsis thaliana), 3'ss of exon 6
---tgtgttgagtcgttgactattaaagtcagtcaaagctgtatattgttgaacgtgtgttatttttgtgtgtacatgtgacttaaaatatgtaattattcagGTTGGATTGGCCATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCAGAAGACCCCTTATTGATTCAGAGATGGGATGCTGAATTTT
|| || | || ||| || ||||| |||| || || | |||| ||||| | ||| ||| || ||| | ||||||| || || | ||||| || || ||||| ||||| ||||| ||||| || || | ||| ||||| || || ||||||||||||||||||||||| || |
gtgagttttcttttgtgcactcttttagtcacccaaaaaattacatgaccaact---tgttcactttgttt---cat-tgatccaa----tgtggt-gttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
upper sequence: GLYMA10G42290.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G25500.1 (Arabidopsis thaliana), 3'ss of exon 6
---tgtgttgagtcgttgactattaaagtcagtcaaagctgtatattgttgaacgtgtgttatttttgtgtgtacatgtgacttaaaatatgtaattattcagGTTGGATTGGCCATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCAGAAGACCCCTTATTGATTCAGAGATGGGATGCTGAATTTT----------
|| || | || ||| || ||||| |||| || || | |||| ||||| | ||| ||| || ||| | ||||||| || || | ||||| || || ||||| ||||| ||||| ||||| || || | ||| ||||| || || ||||||||||||||||||||||| || |
gtgagttttcttttgtgcactcttttagtcacccaaaaaattacatgaccaact---tgttcactttgttt---cat-tgatccaa----tgtggt-gttcaggtgggtttagGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCTACACTGAGAT
upper sequence: GLYMA10G42290.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g03220.t01 (Vitis vinifera), 3'ss of exon 6
tgtgttgagtcgttgactat-taaagtcagtcaaagctgt----atattgttgaacgtgtgttatttttgtgtgtacatgtgacttaaaatatgtaattattcagGTTGGATTGGCCATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCAGAAGACCCCTTATTGATTCAGAGATGGGATGCTGAATTTT
| | | ||||||| || | | | ||| | || | | | | | || || | ||| || | ||| | |||| | |||| ||| |||| ||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| || |||||||||||||| || |
-actcttgggagatgactatatataacctcattattttgttggggtcttatgaagtttatttgatgcttattatgggatggga--tggaatgtacaattgt--agGTGGGACTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATACATTTGCTATGCAGAAGACCCCTTATTGATCCATAGATGGGATGCTGAGTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaacgtgtgttatttttgtgtgtacatgtgacttaaaatatgtaattattcagGTTGGATTGGCCATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCAGAAGACCCCTTATTGATTCAGAGATGGGATGCTGAATTTT
tgacttaaaatatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgttgagtcgttgactattaaagtcagtcaaagctgtatattgttgaacgtgtgttatttttgtgtgtacatgtgacttaaaatatgtaattattcagGTTGGATTGGCCATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCAGAAGACCCCTTATTGATTCAGAGATGGGATGCTGAATTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- tgttgag
- - - - - - - - - - - - - - - - -agctgta
- - - - - - - - - - - - - - - - - - - - - - - - -acgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactt