Sequence
atgc intronic sequence ATGC exonic sequence...tcccagccagtagctgcttccaaatgcagtcaatttgtacagacaatcataacctctctctccacatattttgtcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
Basic information
species | Glycine max |
transcript | GLYMA20G26160.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G26160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g03144.1 (Oryza sativa), 3'ss of exon 4
tcccagccagtagctgcttccaaatgcagtcaatttgtacagacaatcataacctctct----ctccacatattttgtcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
| |||| ||| | | || || ||| | || ||| | | | || | | ||||| | | | | | | ||| ||| |||||||| |||||||| ||||| |||||||||||||| ||| |||||| ||||||| || || || || ||||| ||||||||||||||||||||
tgattagagatagcgcattcattggtcctttgatgtg-acaaaagtgcaaaacataagtgagattgcataaactttgttcaca---tatgtgccatccttttagGTCTTGATGCGTTCCAGGCAGAGAAGGTCATGGAAACTCTTAGACAGCTTGCAGAAGATGGACACACGGTGATATGTTCTATACATCAGCCAAGAGGTTC
upper sequence: GLYMA20G26160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G119345_T01 (Zea mays), 3'ss of exon 4
tcccagccagtagctgcttccaaatgca-gtcaatttgtacagacaatcataacctctctctccacatattttgtcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
|| | |||||| || || | || || | | | || | | | ||||||| | | ||| | ||| |||| ||| |||||||||||||| |||||||| |||||||| ||||| | |||||||| || ||||| || ||||| || ||||||||||| ||||||||||||||
tcataaacagtagtcatcaacatctgtttggtcatctgacaatatgaaaatgtcaaatattaagttatatttttttgtatgtatgtgatttgtctttt-agGCCTTGATGCCTTCCAAGCTGAGAAGGTCATGGAGACTCTTCGTCAACTTGCTCAGGATGGGCACACTGTTATCTGTTCGATACACCAGCCAAGAGGTTC
upper sequence: GLYMA20G26160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 4
tcccagccagtagctgcttccaaatgcagtcaatttgtacagacaatcataacctctctctccacatattttg----tcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
||| ||| | | | ||| ||| | || | | | | | | || | | || || | | || || || |||||| |||||||||||||||||||||||||| ||||| || | ||| | |||||||| ||||| |||||||| || || || ||||| ||||| ||||||||
---------gtaaatgcct---agtctgtctgattc---tgaacattgatggattgttttaaaaaagaattagaggatgataaaatattcttgtg-gtcttcagGGCTTGATGCCTTCCAGGCTGAGAAAGTGATGGAGACATTGCAAAAGCTTGCACAGGATGGACATACTGTGATCTGCTCCATACACCAGCCTAGAGGTTC
upper sequence: GLYMA20G26160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g04670.t01 (Vitis vinifera), 3'ss of exon 4
-----tcccagccagtagctgcttccaaatgcagtcaatttgtacagacaatcataacctctctctccacatattttgtcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
| | || || | || | | | ||| || || | || || ||||| | || | | ||| || |||||| ||||| |||||||| || || || ||||| || |||| || ||||||||| ||||| || |||||||||||||| ||||| ||||| ||| ||||
ttctttttttctccataactattggcatgagagttttgctagtagtgaagcccacataagcttct-----atggtttgtaaccaaataactgatggtgcttgtagGACTCGATGCTTTCCAGGCAGAAAAGGTGATGGAGACACTCCGACTACTTGCACAGGATGGACACACTGTAATTTGTTCCATACACCAGCCTAGAAGTTC
upper sequence: GLYMA20G26160.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ08843 (Selaginella moellendorffii), 3'ss of exon 4
tcccagccagtagctgcttccaaatgcagtcaatttgtacagacaatcataacctctctctccacatattttgtcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
||||| | | | || || | | | | | || | || || || | ||||||||||||| || || || ||| |||| |||||||||||| | ||||||| |||||||||||||| || | |||||||| |||||||| | || ||
--------------------------------gtttgttttgtgctacgcagtttcggagtc-atttctgattccttggactttttcccttgg---ccagGACTTGATGCATTTCAAGCAGAGCAAGTGATGGAAACTCTCAAGAAACTTGCCCAAGATGGTCATACCGTTGTGTGTTCGATTCATCAGCCTCGTGGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcataacctctctctccacatattttgtcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
tcataac putative branch site (score: 2)
ttttctgtgttttc putative PPT
acatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcccagccagtagctgcttccaaatgcagtcaatttgtacagacaatcataacctctctctccacatattttgtcatgaagttgttttctgtgttttcagGACTTGATGCCTTCCAGGCTGAGAAAGTCATGGAAACTCTCCAACAACTTGCACAAGATGGTCATACTGTAATTTGTTCGATACATCAGCCAAGAGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
-cccagcc
- - - - - - -ctgcttc
- - - - - - - - - - - - tgcagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatg