Sequence
atgc intronic sequence ATGC exonic sequence...taatcttcaaaaacataaggttacaacaaaagttagagcttgcagaaacaatgactttactaaaattaaaactaaacaattggagtgtgacttcatgcagGACTATTAAGGTGTGGGAAGAGTTGCAGGCTGAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGCCTTTTATCTGAATATGAAGAAAAAATGGT
Basic information
species | Glycine max |
transcript | GLYMA14G39530.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39530.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g14670.1 (Oryza sativa), 3'ss of exon 1
taatcttcaaaaacataaggttacaacaaaagttagagcttgcagaaacaatgactttactaaaattaaaactaaacaat-tggagtgtgacttca--tgcagGACTATTAAGGTGTGGGAAGAGTTGCAGGCTGAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGCCTTTTATCTGAATATGAAGAAAAAATGGT
||| || ||| | | | | | | | || | | ||| |||| | | || | | | || || |||||| | | ||||| |||||||| ||||||||||||||||| || ||| ||||||| ||| | ||||| ||||| | || || | || || | ||
-----gtcaggaaagaaagctcgct-cgctcgctcgctcgc-cattgatgccccccatacgcgaattgcatgttgacggtgtcgttcatgggcgcatctgcagGGTTGCTGAGGTGCGGGAAGAGCTGCAGGCTGAGGTGGACCAACTACCTGAGGCCCGACCTCAAGAGGGGCCTCCTCTCCGACGACGAGGAGCGGCTCGT
upper sequence: GLYMA14G39530.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g49986.1 (Oryza sativa), 3'ss of exon 1
---------------------------------taatcttcaaaaacataagg---ttacaacaaaagttagagcttgcagaaacaatgactttactaaaattaaaactaaacaattggagtgtgacttcatgcagGACTATTAAGGTGTGGGAAGAGTTGCAGGCTGAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGCCTTTTATCTGAATATGAAGAAAAAATGGT
| || | ||| || | | | || | ||| | | | | ||| | | | | | ||| ||| | ||||| || | |||||||||||||| ||| ||||||||||||| || ||| || |||| ||| | ||||| ||||| | || ||| | || || || ||||
gtgcatgagcatgcatgaccatgtgtttccatctgatgcgcgaaagggaaaaggattcgcgttaacatgcagatcgtcctgcaactgcaatgggagtgactgtgccttcgggtttttgctatgtttcact-cgcagGGCTGCTCAGGTGTGGGAAGAGCTGCCGGCTGAGGTGGACGAACTACCTGCGGCCCGACCTCAAGAGGGGCCTCCTTTCCGAAGAGGAGGAGAAGCTGGT
upper sequence: GLYMA14G39530.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 1
-taatcttcaaaaacataaggttacaacaaaagttagagcttgcagaaacaatgactttactaaaattaaaactaaacaattggagtgtgacttca-tgcagGACTATTAAGGTGTGGGAAGAGTTGCAGGCTGAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGCCTTTTATCTGAATATGAAGAAAAAATGGT
| || | | | | ||| || || | || | | | | | | | ||| | || | | | || | |||||||||||| ||||||| || || ||||| | || |||| |||||| || || || || ||||| ||||| |||||||| |||||||||||| ||| |||
acgctattatttggtttttaatcaattttagttttatagtttttaagtttaa--attaaattgatcgttgatttaattactttgtttacaaattaaatgcagGACTATTGCGGTGTGGTAAAAGCTGCAGATTAAGATGGATAAATTATTTAAGACCTGATTTAAAAAGAGGTCTTTTATCAGAATATGAAGAACAAAAGGT
upper sequence: GLYMA14G39530.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0006g00450.t01 (Vitis vinifera), 3'ss of exon 1
---taatcttcaaaaacataaggttacaacaaaagttagagcttgcagaaacaatgactttactaaaattaaaactaa--acaattggagtgtgacttcatgcagGACTATTAAGGTGTGGGAAGAGTTGCAGGCTGAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGCCTTTTATCTGAATATGAAGAAAAAATGGT
| || ||| | || | | | | | || || | | | | ||| || || ||||||| | ||| ||| | | ||||||||| |||||||||||||||||||||||||| || |||||||| || ||||||||||||| || ||||| || || || || | |||||| | |||||
aaccgaaatttcaaagtacaaaga---aggagataatcaccttttcaaatgcctttatttttctctcat--aaactaattgcgattatggtgggtatcattgcagGACTGTTAAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACAAACTATCTGAGGCCAGACTTGAAAAGAGGTCTGTTGTCAGATTTTGAAGAGCAGATGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacaatgactttactaaaattaaaactaaacaattggagtgtgacttcatgcagGACTATTAAGGTGTGGGAAGAGTTGCAGGCTGAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGCCTTTTATCTGAATATGAAGAAAAAATGGT
actttactaaaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatcttcaaaaacataaggttacaacaaaagttagagcttgcagaaacaatgactttactaaaattaaaactaaacaattggagtgtgacttcatgcagGACTATTAAGGTGTGGGAAGAGTTGCAGGCTGAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGCCTTTTATCTGAATATGAAGAAAAAATGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - aaaaaca
- - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - -gcttgca
- - - - - - - - - - - - - - - - - - - - - - gaaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagtgtg