Sequence
atgc intronic sequence ATGC exonic sequencegcacgtcctcctattcccttccctttcactcctctgcgtccgattagttactgttctattctgctccgattcattactaattgatgattactattgacaatgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC
Basic information
species | Glycine max |
transcript | GLYMA05G30130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 1
gcacgtcctcctattcccttccc--tttcactcctctgcgtccgat----tagttactgttctattctgctccgattcatt--------actaattgatgattactattgac--------------------aatgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC
| || ||| || || ||| | | | | | | ||| | | | ||| | ||| | || | |||||| | |||| || || ||| |||||||||| || || |||||||| || |||||||||||||| |||||||| |||||||||||||| ||||| |||||||| |||||||| ||||||||||| ||
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagggaatgcagGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAACATCGAGTCG
upper sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 3'ss of exon 1
gcacgtcctcctattcccttccct--ttcactcctctgcgtccga----ttagttactgttctattctgctccgattcatt--------actaattgatgattactattgac--------------------aatgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC
| || ||| || || ||| | | | | | | ||| | || ||| | ||| | || | |||||| | |||| || || ||| |||||||||| || || |||||||| || |||||||||||||| |||||||| |||||||||||||| ||||| |||||||| |||||||| ||||||
gtgagttatccaatgccgttctccgcctgaattcgttccgtgtggtgtgtttgttgcggttgcttgctcaactgattcaatcaatcggggtggattgtatttttcttttgtttggggggggggggggaagGGAATGCAGGGTGCGGCGCCACACGATCTCTGTGTTCGTCGGCGACGAGAGCGGGATGATAAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGGTACAAC---------
upper sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------gcacgtcctcctattcccttccctttcactc-ctctgcgtccgattagttactgttctattctgctccgattcatta--ctaattgatgattactattgac----aatgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC
| || | | | | | || | | | || || | ||| ||||| | | || | | | | || | | | | || | |||||||||| || || ||||||||||| ||||||||||| || |||||||| ||||| |||||||| ||||| |||||||| |||||||| ||||||||||| ||
gtaagcgctcccctccccttgcccgccgaacttccgcctcttcgttttcttaattaaatctcttcgcggcgcgcgggactcgtgttgtttgtgcgcgcgccgccctttctgtttctgtttctgttttcttcttctggtgaggctgggtcgggtctctgagtggcgccaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCCGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG
upper sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 1
--------------------------gcacgtcctcct-attcccttccctttcactcctctgcgtccgattagttactgttctattctgctccgattcattactaattgatgattactattgacaa-tgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC
|| |||||| || | | || || | | ||| |||| | | | |||| || | | | || | | | || || | ||| |||||||| || || ||||||||||| ||||||||||| || |||||||| ||||| |||||||| || || |||||||| |||||||| ||||||||||| ||
gtaagcaccccaccttgcccgccgaaatgcggcctccttgtttcttaatctctcgcggc---gcgcgggatttctccgttcctttttcttcttctgatgac-gctgctcgg-gttttctggcgtcaaatgcagGGTGCGGCGCCACACGATTTCGGTGTTCGTCGGGGACGAGAGCGGCATGATCAACCGGATCGCAGGGGTGTTCGCCAGGAGAGGCTACAACATCGAGTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttctattctgctccgattcattactaattgatgattactattgacaatgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC
attcattactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcacgtcctcctattcccttccctttcactcctctgcgtccgattagttactgttctattctgctccgattcattactaattgatgattactattgacaatgcagGGTTCGTCGACACACGATTTCCGTGTTCGTCGGCGATGAGAGCGGAATGATAAACCGGATTGCCGGCGTGTTCGCTAGGAGAGGATACAACATCGAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT