Sequence
atgc intronic sequence ATGC exonic sequencegtacaattcagttaattgtcctgatggcattcttttctttgatatattacctaaaaagatatatattgatgaaaatactcatgagataggtctagctcataaattcttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
Basic information
species | Glycine max |
transcript | GLYMA05G04940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
gtacaattcagttaattgtcctgatggcattcttttctttgatatattac-ctaaaaagatatatattgatgaaaatactc-atga---gatagg--------tctagctcataaattc-ttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
|||| | | | | | | || | | | || ||||| | || || | || || | | ||| || | ||||| | | || || || |||||||||| ||||||||||||||||| ||||| ||||| ||||| || ||||||||||||||| | ||| |||| | | | | ||||||||||| || ||||| |
gtactaat--atcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
upper sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
gtacaattcagttaattgtcctgatggcattcttttctttgatatattacctaaaaag-atatata-ttgatgaaaatactcatgagataggtctagctcataa-attcttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
|| | || |||| | | |||| ||| | || || | || || || || ||| | | || | || | | |||||||| ||||||||||||||||| ||||| ||||| |||||||| |||||||| |||||||| || ||||| | ||| | ||||||||||| || ||||| |
-------------aacagat---ataagattcctgccattga-ataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
upper sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 3
gtacaattcagttaattgtcctgatggcattcttttctttgatatattacctaaaaagatatatattgatgaaaatactcatgagataggtctagctcataaattcttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
|| ||| | || | | |||| || | | | | | ||| | | | | | | || | | | |||||||| ||||| ||||| ||||| ||||| |||||||||||||| |||||| | |||||||| || ||||| | ||| | ||||||||||| || ||||| |
------catagaagattcataccacggaaggaacacca--gata-gttgctttgtacaagctttatcttc-----tttttgttaacttattacagacacaatacgatcttgcagGGCATGTTCGTTCCAGCTATAAAAGGCCAAGGAACTGAGGAGCAGCAGCACAAGTGGTTACCACTGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
upper sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 3
gtacaattcagttaattgtcctgatggcattcttttc-tttgatatattacctaaaaagatatatattgatgaaaatactcatgagataggtctagctcataaattcttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
| | | | | | | || ||| || | | | || ||||| | |||| | || | ||| | | | ||||||||||||| |||||||| || || || || || ||||| |||||||||||||||||| | |||| |||||||||| || ||||| |||||||| |
--------------------------gtactacctgcgtctcatttatcttctggagaca-ggattttgattctttgattcattgtttttgtat--ctc------tgctctatagGGAATGTTTGTGCCTGCTATTAAGGGGCAGGGTACAGAGGAGCAGCAGAAGAAGTGGTTGTCGCTGGCCAATAAGATGCAGATTATTGGGTGTTATGCAC
upper sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacaattcagttaattgtcctgatggcattcttttctttgatatattacctaaaaagatatatattgatgaaaatactcatgagataggtctagctcataaattcttttg--cagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
| | | | | | || || | | ||| || | | | | ||| | | || | || ||||||||||||| ||||| || ||||||||||| || ||| |||| || | ||||||||| |||| ||| ||||||||| |||||||| |||||||| |
------------------------------------gtataacacaaaatttacaa---tttcccttgggtggtttaattagaattttggtgttgaattggttttgtggtggatagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatattgatgaaaatactcatgagataggtctagctcataaattcttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
tattgat putative branch site (score: 3)
ttcttttgc putative PPT
tcataaattctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaattcagttaattgtcctgatggcattcttttctttgatatattacctaaaaagatatatattgatgaaaatactcatgagataggtctagctcataaattcttttgcagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG