Sequence
atgc intronic sequence ATGC exonic sequencegtaatttcttcttttctttgttttccttttagtgatttggctgtaatgttctgttttttgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53390.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G096070_T01 (Zea mays), 3'ss of exon 2
gtaatttcttcttttctttgttttccttttagtgatttggctgtaa--tgttctgttttt--tgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
| || || | || ||||| || ||| || || | |||||| ||| ||| ||| | || | | || ||| ||||||||| ||||||| ||||||||||| || |||||||| |||| ||||| || || || || || || || || || ||| | | |||||| || |
--------gtattcactattcagtcattttactggaatggatgcaagccacacagtttttgatgtcttgcttttttc-tgatcatctg-----tttacttgcactagGATCCACTAAAGTCCATCCATTTCAGCAACTCAAACCCACTGTGCCATGCATTCGACCCAGAGGCCAAAGAGGGACACGACCTGATCATTGGGATGGGAT
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 2
gtaatttcttcttttctttgttttccttttagtgatttggctgtaatgttctgttttttgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
| | | | | ||| || | ||| | |||| ||| || || ||||| ||| || ||||||||||| |||||||||||||| |||||||||||||| |||||||| ||||| ||||||| |||| |||||||||||||||| || | ||||| |||||
-----------------gtataatgatcgggttagggtggatggattgtaaggattttgactttattcatgaga----ggttt------cttgttcaatgtagGATCCTGTAAAGTCTATCCACTTCAGTAATTCAAATCCTATGTGCCATGCATTTGATCAGGATTCTAAGGATGGGCATGATTTGATCATTGGCTTGAATA
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 2
gtaatttcttcttttctttgttttccttttagtgatttggctgtaatgttctgttttttgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
| | || || || | ||| || | ||| | |||| |||| || || ||||| ||| || ||||||||||| |||||||||||||| |||||||||||||| |||| ||| ||||| ||||||| |||| ||||||| |||||||| || | ||||| |||||
-----------------gtatattggttg-ggttaggtggatggattgtatttattttgattttattcacgaga----ggttt------cttgttcaatgtagGATCCTGTAAAGTCTATCCACTTCAGTAATTCAAATCCTACGTGCCATGCATTTGATCAGGATTCTAAGGACGGGCATGATTTGATCATTGGCTTGAATA
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G36480.1 (Glycine max), 3'ss of exon 2
gtaatttcttcttttctttgttttccttttagtgatttggctgtaatgttctgttttttgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
| ||| | ||| ||| || |||| | |||| | |||| || | | ||||| ||| || ||||||| || |||||||||| || |||||||| || || ||| |||| || || ||||||| ||||||||||||||||||||| || || ||||| |||| |
------------gtatattggtcggagtttgatgaattt----taatataagaattttggatttgcttc---atcagaggttt------cttgttgcgtgtagGACCCCATAAAGTCTATTCACTTCAGTAACTCGAATCCTGTGTGCCACGCATTTGATCAGGATGCTAAGGATGGGCATGATTTGCTCATTGGTTTGAACT
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G33740.1 (Glycine max), 3'ss of exon 2
gtaatttcttcttttctttgttttccttttagtgatttggctgtaatgttctgttttttgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
|| | | || |||| | || | | | |||| | |||| || | ||| ||| ||| || ||||||| || |||||||||| || |||||||| || || ||| |||| || | ||||||| ||||||||||||||||||||| || || ||||| |||| |
-------------------gtatattggtcag--attttgatggattttaagaattttgggtttgcttcatggttcatgag--aggtttcttgttgcgtgtagGACCCCATAAAGTCTATTCACTTCAGTAACTCGAATCCTGTGTGCCACACGTTTGATCAGGATGCTAAGGATGGGCATGATTTGCTCATTGGTTTGAACT
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 2
gtaatttcttcttttctttgttttccttttagtgatttggctgtaatgttctgttttttgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
||||||| | |||||| | | ||||| | | | | |||| || || || | ||| || ||||| || ||| ||||||||||| |||||||||| ||||| |||||||| || ||| | |||||||| ||||| ||||||||||||||||| ||||| || ||||||||| ||||||
gtaatttgatgttttctg-gctgcggttttaatcaataat---tcatgtcttgcgttggaattggattttgaga----ggtttg------ttttttaatgtagGATCCCATAAAGTCTATACATTTTAGTAATTCGAATCCTGTTTGTCATGCATTTGACCCGGATGCTAAGGATGGACATGATTTGCTTATTGGGTTGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgttttttgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
ctttgat putative branch site (score: 5)
cttcttt CT-rich tract
ttttttgttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttcttcttttctttgttttccttttagtgatttggctgtaatgttctgttttttgttttgttttggaagtaatggtttaggaaacttctttgatgtagGATCCAGTAAAGTCTATCCATTTCAGTAATTCAAACCCTATGTGTCATGCTTTTGATCCGGATGCTAAGGATGGGCATGACTTACTTATTGGGCTGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG