Sequence
atgc intronic sequence ATGC exonic sequencegcacgtcttcctattctgttccctttcactcagtcctctgcgtccggttagttactgttctgttccgattcgttactaattgatgattactaccattgacaatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
Basic information
species | Glycine max |
transcript | GLYMA08G13290.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 1
gcacgtcttcctattctgttccct-------ttcactcagtcctctgcgtc-----cggttagttactgttctgttccgat---tcgttactaattgatgattactaccatt-----------------gacaatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
| || ||| || | |||| | ||| || || || || ||||| || || ||| | | || ||| |||| || || || | |||||||||| ||||| |||||||| || |||||||||||||| |||||||| |||||||||||||| || || |||||||| |||||||| |||||||||||||||
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagggaatgcagGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAACATCGAGTCG
upper sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 1
gcacgtcttcctattctgttccct-------ttcactcagtcctctgcgtc-----cggttagttactgttctgttccgat---tcgttactaattgatgattactaccatt-----------------gacaatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
| || ||| || | |||| | ||| || || || || ||||| || || ||| | | || ||| |||| || || || | |||||||||| ||||| |||||||| || |||||||||||||| |||||||| |||||||||||||| || || |||||||| |||||||| ||||||
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC---------
upper sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 1
------------gcacgtcttcct--attctgttccctt-tcactcagtcctctgcgtccggttagttactgttctgttccgattcgtta--ctaat--tgatgattactaccattgac----aatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
| | | || || | | |||| | || | || ||| | | | | | || ||||| || || || || | || | || | |||||||||| ||||| ||||||||||| ||||||||||| || |||||||| ||||| |||||||| || || |||||||| |||||||| |||||||||||||||
gtaagcaccccaccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggcgcgcggg--atttctccgttcctttttcttcttctgatgacgctgctcgggttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
upper sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------gcacgtcttcct-attctgttccctttcactcagtcctctgcgtccggttagttactgttctgttccgattcgttactaattgatgattactaccattgacaa-tgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
|| || || | |||| | | | | ||| | || | | | | | ||| | | | || | | | | | ||| |||||||| ||||| ||||||||||| ||||||||||| || |||||||| ||||| |||||||| || || |||||||| |||||||| |||||||||||||||
gtaagcgctcccctccccttgcccgccgaacttccgcctcttcgttttcttaattaaatctcttcgcggcgcgcgggactcgtgttgtttgtgcgcgcgccgccctttctgtttctgtttctgttttcttcttctggtgag--gctgggtcgggtctctgagtggcgccaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
upper sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S162_10V6.1 (Physcomitrella patens), 3'ss of exon 1
gcacgtcttcctattctgttccctttcactcagtcctctgcgtccggttagttactgttctgttccgattcgttactaattgatgattactaccattgacaatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
| | | | | |||| | | || | | | | || | ||| | | || ||| | | || ||| |||||| || || |||| || |||||||||||||| || |||||||||||||| ||| | |||||||| || | || | | || |||||||| || ||
-----ttgtgcaacggaaccacggctcacaatgcggggtttgtgggatgcttaatcttttttaggcgagacatc-ctccaagattctca-tagttttgctgcaacagGGTACGCAGATACACTATATCCGTGTTCGTCGGGGACGAGAGCGGAATGATCAACAGAATTGCTGGAGTTATTGCACGACGTGGTTACAACATTGAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactgttctgttccgattcgttactaattgatgattactaccattgacaatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
ttactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcacgtcttcctattctgttccctttcactcagtcctctgcgtccggttagttactgttctgttccgattcgttactaattgatgattactaccattgacaatgcagGGTTCGGCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCTGGCGTGTTCGCGAGGAGAGGATACAACATCGAGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT