Sequence
atgc intronic sequence ATGC exonic sequence...tttctttctgtttcatttggcatatatttacaaacacagctctatatttgagaacaaatactctggtttaatggatcttaccttttatttttatttatagGTTCTCTTGTAAGGCCAAAGGTTGTTAAAAGTGTTCATTTTTGCCCCACCACCGGAAGCTTCACTTCTCGCGAATATCGTGATATTACATCTAATTTGGG
Basic information
species | Glycine max |
transcript | GLYMA05G25980.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G162445_T01 (Zea mays), 3'ss of exon 3
tttctttctgtttcatttggcatatatttacaaacacagc-tctatatttgagaac--aaatactctggtttaatggatcttaccttttatttttattta----tagGTTCTCTTGTAAGGCCAAAGGTTGTTAAAAGTGTTCATTTTTGCCCCACCACCGGAAGCTTCACTTCTCGCGAATATCGTGATATTACATCTAATTTGGG
|| || | || || | | |||| | | || | || | | || | | | | || |||| ||| || | | | |||||| | ||||||||||| |||||||| |||||||| |||||||| || || ||| || || |||||| | || || || ||| | | ||
----ttactagtagtgtt--caagcactggtggacaccatgtttttagtgaagtatctgcacacctttgggtgcta-atattacttttccttctgaaaaaaaaacagGTTCATTGGTAAGGCCAAAAGTTGTTAAGAGTGTTCACTTTTGCCCTGTGACTGGGGCCTTTCTCTCGCGTGAATATAGAGACATCACTTCTTTTGTAGG
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 3
--------tttctttctgtttcatttggcatatatttacaaacacagctctatatttgagaacaaatactctggtttaatggatcttaccttttatttttatttatagGTTCTCTTGTAAGGCCAAAGGTTGTTAAAAGTGTTCATTTTTGCCCCACCACCGGAAGCTTCACTTCTCGCGAATATCGTGATATTACATCTAATTTGGG
| ||| | ||| | | ||| || | | ||| | || | | || || | | | ||| || ||| |||||||| |||||||||||||||||||| ||||| ||||| || | ||||| || || ||| || ||||| || || |||||| | ||
gtaagctcatcattttcactctattcctc-tgcttttcttctgtttcctttgtgttttacgtagaagattttgaacctctgacacatgc--------tttgctttcagGCTCTCTTGTGAGGCCAAAGGTTGTTAAAAGCGTTCACTTTTGTCCATCAACCGGTGAATTTACCAATCGAGATTATCGAGACATAACATCTCACGCTGG
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 3
tttctttctgtttcatttggcatatatttacaaacacagctctatatttgagaacaaat--actctggtttaatgg-atcttacct-----tttatttttatttatagGTTCTCTTGTAAGGCCAAAGGTTGTTAAAAGTGTTCATTTTTGCCCCACCACCGGAAGCTTCACTTCTCGCGAATATCGTGATATTACATCTAATTTGGG
| || || || | ||| | | || || |||| | || || ||| | | |||| |||| ||| | | || | |||||||||||||||||||||||||||||||||||||||| || ||||| | | || | |||||| | || |||||||| |||||||| || ||| ||||
------tttgcttagttataaactaattcatttccttg--tcaattcttgatggtatattgacgttggagcatagatatctaacctgctcatttttcctcatctctagGTTCTCTTGTAAGGCCAAAGGTTGTTAAAAGTGTTCACTTCTGCCCTTCATCTGGGAATTTCACTACCCGTGAATATCGAGATATTACGTCCAATATGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgagaacaaatactctggtttaatggatcttaccttttatttttatttatagGTTCTCTTGTAAGGCCAAAGGTTGTTAAAAGTGTTCATTTTTGCCCCACCACCGGAAGCTTCACTTCTCGCGAATATCGTGATATTACATCTAATTTGGG
atcttac putative branch site (score: 3)
tcttaccttttatttt CT-rich tract
atcttaccttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctttctgtttcatttggcatatatttacaaacacagctctatatttgagaacaaatactctggtttaatggatcttaccttttatttttatttatagGTTCTCTTGTAAGGCCAAAGGTTGTTAAAAGTGTTCATTTTTGCCCCACCACCGGAAGCTTCACTTCTCGCGAATATCGTGATATTACATCTAATTTGGG
- -ctttctg
- - - - - - - - - -gcatata
- - - - - - - - - - - - - - - caaacac
- - - - - - - - - - - - - - - - - - - - - - - - - agaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctggtt