Sequence
atgc intronic sequence ATGC exonic sequencegtatttgacttatcttgtgcattgttgagaagaattttgctgctgtttatgcatatttaattttgatgatgtttgtgtgcagGTTTTGGATTTCGACTTTGAAAAATTCTGTTCTGTCTCCCTGTCAAATTTAAATGTGTATGCATGTTTGGTTTGCGGGAAGTATTACCAAGGGAGAGGGA
Basic information
species | Glycine max |
transcript | GLYMA10G08500.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 1
--gtatttgacttatcttgtgcattgt----tgagaagaatt-ttgct--gctgttt---atgcatatttaattttg-----atgatgtttgtgt-gcagGTTTTGGATTTCGACTTTGAAAAATTCTGTTCTGTCTCCCTGTCAAATTTAAATGTGTATGCATGTTTGGTTTGCGGGAAGTATTACCAAGGGAGAGGGA
|| || ||| ||| | | ||| || | || ||| | ||| ||| ||| ||| | | ||| || ||| | | | |||| | ||||| || ||||| || ||||| || ||||| | ||||| || || |||||||||||||||||||| || |||||||||||||| |||||
atgttttacactcttctggcagaatgtgtgctggactgtatcattgatgggctatttcacatgttcattgattgttgtatatattttgtctacattgtagGTCCTTGATTTTGATTTTGAGAAGTTCTGCTCAATCTCCTTATCAAACTTGAACGTGTATGCATGTTTGGTTTGTGGAAAGTATTACCAAGGAAGAGGCT
upper sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 1
------------------gtatttgacttatcttgtg---cattgttgagaagaattttgctgctgtttat-gcatatttaattttgatgatgtttgtgtgcagGTTTTGGATTTCGACTTTGAAAAATTCTGTTCTGTCTCCCTGTCAAATTTAAATGTGTATGCATGTTTGGTTTGCGGGAAGTATTACCAAGGGAGAGGGA
| ||||| | || |||| || | ||| | | |||| || | || |||||| || | | |||||||| | ||||| || || || || |||||||| ||||| |||||||||| ||||||||||| || ||||| || || || |||| |||||| ||||||
atctggtccatgtaacatttttttgatatggtccatgtaacattttttcattacgtcttgtggttatttacagctgagttcattttg----tgctgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT
upper sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S7_57V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------gtatttgacttatcttgtgcattgttgagaagaattttgctgctgtttatgcatatttaattttgatg---atgtttgtgtgcagGTTTTGGATTTCGACTTTGAAAAATTCTGTTCTGTCTCCCTGTCAAATTTAAATGTGTATGCATGTTTGGTTTGCGGGAAGTATTACCAAGGGAGAGGGA
| || || ||||| | ||| | | |||| | | ||| | || || || |||| ||||| |||||||||||||||| ||||| || || ||||| || || ||||| |||||||| ||||| | || |||||||| |||| ||||| ||||
gatatgttttttgaattggtttcctgctcttggttgtatccaagatggtcaactttactgtggagtagtctttcaacttactggatattgttgtcctcagGTGCTGGATTTCGACTTTGAGAAATTTTGCTCGGTCTCACTTTCCAATTTGAATGTGTACGCATGCCTTGTGTGCGGGAAATATTTTCAAGGACGAGGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaagaattttgctgctgtttatgcatatttaattttgatgatgtttgtgtgcagGTTTTGGATTTCGACTTTGAAAAATTCTGTTCTGTCTCCCTGTCAAATTTAAATGTGTATGCATGTTTGGTTTGCGGGAAGTATTACCAAGGGAGAGGGA
ttttgat putative branch site (score: 4)
tttatgcatatttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgacttatcttgtgcattgttgagaagaattttgctgctgtttatgcatatttaattttgatgatgtttgtgtgcagGTTTTGGATTTCGACTTTGAAAAATTCTGTTCTGTCTCCCTGTCAAATTTAAATGTGTATGCATGTTTGGTTTGCGGGAAGTATTACCAAGGGAGAGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG