Sequence
atgc intronic sequence ATGC exonic sequencegtatgggcttttacttattatacgactgagaattgcatatacattgttttcccttttcttaccagttctcaagttactatatgactgctgtgctatcaaatagGGAAGACGTTACTTGCGAAAACACTGGCTCGTTTTGTGAATGTTCCCTTTGTCATTGCTGATGCTACTACCCTAACACAGGCAA
Basic information
species | Glycine max |
transcript | GLYMA20G35600.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G101791_T02 (Zea mays), 3'ss of exon 3
-----------------gtatgggcttttacttattatacgactgagaattgcatatacattgttttcccttttcttaccag------ttctca--agttactatatgactgctgtgcta-tcaaatagGGAAGACGTTACTTGCGAAAACACTGGCTCGTTTTGTGAATGTTCCCTTTGTCATTGCTGATGCTACTACCCTAACACAGGCAA
| | || | |||| | ||| | | || | || | | | || || |||| ||| ||| | || | | | | ||| || || |||||||| || ||| | ||||||||||||||||| || ||||| ||||||||||| || || |||| |||
gtaaggcatctgcaaccatttaaagttggatttatgtcagctctggctactatatttg-atcaactcaaatgtctgtaaaaggaagtgcactcagcagtatttatttttatggttcatttctttcacagGTAAAACTTTACTTGCAAAGACATTAGCTCGTTTTGTGAATGTACCATTTGTAATTGCTGATGCAACGACATTAACCCAG----
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G050186_T05 (Zea mays), 3'ss of exon 3
-----------------------------------------gtatgggcttttacttatta-tacgactgagaattgcatatacattgttttcccttttcttaccagttctcaagttactatat-gactgctgtgctatcaaatagGGAAGACGTTACTTGCGAAAACACTGGCTCGTTTTGTGAATGTTCCCTTTGTCATTGCTGATGCTACTACCCTAACACAGGCAA
| | ||| | ||| | | ||| | | | ||| || | || | | || | ||| | ||| | ||| | | | | | ||| || || |||||||| || ||| | ||||||||||||||||| || ||||| ||||||||||| || || | || |||
gtaagacatctgtaaccatttaaaattttaaagttggatttatgtcagctctgactagtgactactattttggattaactaaa-atgtctgtaaaaagaaagggcactcagcaatattttattttgacggttcatttctttcacagGTAAAACTTTACTTGCAAAGACATTAGCTCGTTTTGTGAATGTACCATTTGTAATTGCTGATGCAACAACATTGACCCAG----
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgggcttttacttattat--acgactgagaattgcatatacattgttttcccttttcttaccagttctcaagttactatatgactgctgtgctatcaaatagGGAAGACGTTACTTGCGAAAACACTGGCTCGTTTTGTGAATGTTCCCTTTGTCATTGCTGATGCTACTACCCTAACACAGGCAA
||||| |||||| | || | | ||| || ||| | || | | | | | | | | | | || | || ||| |||||||||| ||||| || || || |||| | |||| |||||||| ||||||||||||||||| ||||| || || |||
gtatgagcttttgtgttttcctgatcatattctattttttacttcccatttgcactctccctgctgacagtgacatgatagtttatttgattctttaacaa-tagGGAAGACATTACTCGCAAAGACTTTGGCGAGGCTTGTAAATGTTCCTTTTGTCATTGCTGATGCAACTACACTGACTCAG----
upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------gtatgggcttttacttattatacgactgagaattgcatatacattgttttcccttttcttaccag--ttctcaagttactatatgactgctgtgc-------tatcaaatagGGAAGACGTTACTTGCGAAAACACTGGCTCGTTTTGTGAATGTTCCCTTTGTCATTGCTGATGCTACTACCCTAACACAGGCAA
|| | | | | |||| || | |||||| ||| | | || || | || || ||| | | | ||| | ||| ||| || || |||||||| |||||||| ||||||||||||||||| |||||||||||||||||||| || ||||| ||||||
gtataggccctattttatgatttgagtttagttgtggcataaattgaacactggcagcttcagatctgaagatatctattacattatttcttagtgtgataagaggctgctgaatttagaccaccattctaatgcacattaacttgaaacagGAAAAACATTACTTGCAAAAACACTTGCTCGTTTTGTGAATGTGCCCTTTGTCATTGCTGATGCAACAACCCTTACACAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcccttttcttaccagttctcaagttactatatgactgctgtgctatcaaatagGGAAGACGTTACTTGCGAAAACACTGGCTCGTTTTGTGAATGTTCCCTTTGTCATTGCTGATGCTACTACCCTAACACAGGCAA
ttcttac putative branch site (score: 2)
ttactatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgggcttttacttattatacgactgagaattgcatatacattgttttcccttttcttaccagttctcaagttactatatgactgctgtgctatcaaatagGGAAGACGTTACTTGCGAAAACACTGGCTCGTTTTGTGAATGTTCCCTTTGTCATTGCTGATGCTACTACCCTAACACAGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT