Sequence
atgc intronic sequence ATGC exonic sequence...aaaaaaaagccagaaataaacaatcaaacatgcactaagaactaagaagggtccttaattttgattcagaatctcataatgaattgatttgttgacacagTGGCGACCCCAAAGCAGATAAGGGAGTTGATGAAGGTTGACGGTTTGACCAATGATGAAGTTAAAAGCCATTTGCAG
Basic information
species | Glycine max |
transcript | GLYMA17G12720.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12720.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g08160.1 (Oryza sativa), 3'ss of exon 2
------------------------aaaaaaaagccagaaataaacaatcaaacat-gcactaagaactaagaagggtccttaattttgattcagaatct-cataatgaattgatttgttga----cacagTGGCGACCCCAAAGCAGATAAGGGAGTTGATGAAGGTTGACGGTTTGACCAATGATGAAGTTAAAAGCCATTTGCAG
| ||| ||| | || | | | || || | || | | | || || || | | | | || || ||| | |||||||||||| |||||||| | ||| ||||||||||||| || |||||||||||||| || ||||||||| | |||
gtacagtacacctacacatgtaactcgatcaagatcgaacaccatgattacatgccgtaccaaagatgaaaagacaacaaacaaattaatcttgagcttgcgtttttgttttgttctttgcaaattaaagTGGCGACCCCGAAGCAGATTCGCGAGCTGATGAAGGTTGATGGATTGACCAATGATGAGGTGAAAAGCCATCTCCAG
upper sequence: GLYMA17G12720.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G348238_T01 (Zea mays), 3'ss of exon 2
----aaaaaaaagccagaaataaacaatcaaacatgcactaagaactaagaagggtccttaattttgattcagaatc-tcataatgaa---ttgatttg---ttgacacagTGGCGACCCCAAAGCAGATAAGGGAGTTGATGAAGGTTGACGGTTTGACCAATGATGAAGTTAAAAGCCATTTGCAG
| | | || | | | ||| | ||| | || | || | | || || ||| | | || || ||| || ||| | |||||||||||| |||||||| | ||| |||||||||| || || |||||||||||||| || ||||||||| | |||
gtacagacactggcatgccacagacactttgctatgttagacaaaatgccaaacgcatgcatgcgtgtcccatgatcatgacaaataatacttgtttcctgcttgcaaaagTGGCGACCCCGAAGCAGATCCGCGAGCTGATGAAGGTGGATGGATTGACCAATGATGAGGTGAAAAGCCATCTCCAG
upper sequence: GLYMA17G12720.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G03500.1 (Arabidopsis thaliana), 3'ss of exon 2
aaaaaaaagccagaaataaacaatcaaacatgcactaagaactaagaagggtccttaattttgattcagaatctcata-atgaattgatt-tgttgacacagTGGCGACCCCAAAGCAGATAAGGGAGTTGATGAAGGTTGACGGTTTGACCAATGATGAAGTTAAAAGCCATTTGCAG
| ||| ||| ||| || | | | || | | || | | | | | | || || ||| || | | ||||||| || || || || |||||||| | ||||| ||||| |||||||||||||||||||| ||||||||| | |||
--attaaatatagattaaaataaccttgttaacctaataaaaagtgtttaatttttgaatcgaacttgtatccgtatttatatgttggttatatcattgcagTGGCTACACCTAAACAAATAAGGGAACTCATGAAAGTTGATGGTTTGACCAATGATGAAGTCAAAAGCCATCTCCAG
upper sequence: GLYMA17G12720.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g04600.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------aaaaaaaagccagaaataaacaatcaaacatgcactaagaactaagaagggtccttaattttgattcagaatctcataatgaattgatttgttgacacagTGGCGACCCCAAAGCAGATAAGGGAGTTGATGAAGGTTGACGGTTTGACCAATGATGAAGTTAAAAGCCATTTGCAG
||||||| || |||| | || ||||||| || | | | | | || || | |||||| | || | | | | | || |||||||| ||||||||||| || || ||| ||||||| ||||||||||||||||||||||||||||||||||||||||||
gtaatttgcttgtttttatgatatggtgactatggtcttagaaaagaaaaaggagaaaaaaaacctaaaatga-cagtcaaacaatcatcagcgaatcatcattgttgctattattgatt-----tttcttttttgttgtgataatggaaacagTGGCCACCCCAAAGCAAATCAGAGAGCTGATGAAAGTTGACGGTTTGACCAATGATGAAGTTAAAAGCCATTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagggtccttaattttgattcagaatctcataatgaattgatttgttgacacagTGGCGACCCCAAAGCAGATAAGGGAGTTGATGAAGGTTGACGGTTTGACCAATGATGAAGTTAAAAGCCATTTGCAG
tgttgac putative branch site (score: 3)
ataatgaattgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaaaaagccagaaataaacaatcaaacatgcactaagaactaagaagggtccttaattttgattcagaatctcataatgaattgatttgttgacacagTGGCGACCCCAAAGCAGATAAGGGAGTTGATGAAGGTTGACGGTTTGACCAATGATGAAGTTAAAAGCCATTTGCAG
aaaaaaa
- - - - - - -aaataaa
- - - - - - - - - - - - - - catgcac