Sequence
atgc intronic sequence ATGC exonic sequence...tagatctctctcttttgtttcctttgtgataaaactgaaactgatcaaggttttaatttgttgttgttcattgtttcatgtgtaatgtaacatttggcagTTTGTTCAAGGAATGCCCACACCCTGATGATAAGCAGAGGCTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
Basic information
species | Glycine max |
transcript | GLYMA01G01850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 3
--------tagatctctctcttttgtttcctttgtgataaaactgaaa------ctgatcaa--ggttttaatttgttgttgtt--cattgt----ttcatgtgtaatgta---acatttg-----gcagTTTGTTCAAGGAATGCCCACACCCTGATGATAAGCAGAGGCTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
| ||||| |||| | ||||| | || | || | |||| | || | ||| ||| | ||||| | | || || ||| |||| |||||||||| ||||| || || || || |||||| ||||||| |||||||| ||| |||| || ||||| ||||||||||||||||||||||||||
gtacggttttcatctccatcttcttcttcctcttcaatgccattgccagccgtttcgatcgattcgtctccattaaaccttgctgatattgtgatactgacaagtggcgtgcatgcatccatccatgcagGCTGTTCAAGGAGTGCCCGCATCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAACTGGGCCTCAAACCTCGCCAGGTCAAGTTCTGGTTCCAGAAT
upper sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G123140_T04 (Zea mays), 3'ss of exon 2
------------------------------------tagatctctctcttttgtttcctttgtgata-aaactgaaactgatcaaggttttaatttgttgttgttcattgtttcatgtgtaatgtaacatttggcagTTTGTTCAAGGAATGCCCACACCCTGATGATAAGCAGAGGCTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
|| | | || | ||| | | || || || || ||| | | | || || | || || | | || ||| |||||||||| ||||| ||||| || || |||||| ||||||| |||||||| || |||| || ||||| |||||||||||||||||||||||||||
gtaagacacacacatatatacgcttgccttttcatatataataataatcttcttctccgatatattataatctcttacggatgcatgcatggcaatggcaatggccggcattgcacggacgacata----cgcacagGCTGTTCAAGGAGTGCCCGCACCCGGACGACAAGCAGCGGCTGAAGCTGAGCCAGGAGCTGGGGCTCAAACCCCGCCAGGTCAAGTTCTGGTTCCAGAAC
upper sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g02030.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------tagatctctctcttttgtttcctttgtgataaa--actgaaactgatcaaggttttaatttgttgttgttcatt-gtttcatgtgtaatg-taacatttggcagTTTGTTCAAGGAATGCCCACACCCTGATGATAAGCAGAGGCTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
| | | |||| | ||| | | | || | | | | | | | | | | ||| || | | ||| ||||||| |||||||||||||||||||| ||||| ||||||||| ||||||| ||||| ||| | || || ||||| ||||| |||||||| |||||||| |||
gtatgctactatttctctctcactctcttcaaaaacatggttcttatacttcaatcacaacccattacgcataaatgttgggaaaatcacctaaactcacactctagttgcaccaccgtcactcattttttgcagTTTATTCAAGGAATGCCCACACCCAGATGACAAGCAGAGGATGAAACTCAGCCAAGAACTTGGCCTCAAACCACGCCAAGTCAAGTTTTGGTTCCAAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaggttttaatttgttgttgttcattgtttcatgtgtaatgtaacatttggcagTTTGTTCAAGGAATGCCCACACCCTGATGATAAGCAGAGGCTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
atgtaac putative branch site (score: 3)
ttttaatttgttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagatctctctcttttgtttcctttgtgataaaactgaaactgatcaaggttttaatttgttgttgttcattgtttcatgtgtaatgtaacatttggcagTTTGTTCAAGGAATGCCCACACCCTGATGATAAGCAGAGGCTGAAACTGAGCCATGAATTGGGTCTTAAACCGCGCCAGGTCAAGTTCTGGTTCCAGAAC
- - -ctctctc
- - - - - - - -tgtttcc
- - - - - - - - - - - - - -gataaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttg