Sequence
atgc intronic sequence ATGC exonic sequencegtaacttttctttacagtctacttcatttttgattcttacatgtcgaaactctatcgctacttcatatataactggctcatgagatgatatgtaacaagtaggggttttagcatcgaattgctatgtgttagatgcagtttttgatgactgtatatatgatcgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38960.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 3
gtaacttttctttacagtctacttcatttttgattcttacatgtcgaaactctatcgctacttcatatataactggctcatgagatgatatgtaacaagtaggggttttagcatcgaattgctatgtgttagatgcagtttttgatgactgtatatatgatcgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
| || ||| || || ||| | | | | || | ||| | || || | | | | | || |||||| || | ||||||| ||||| || || ||||||| || ||||||||||| ||||||||||||| ||| ||||| ||||| |||||||| ||||| ||| |||||
-------------------------------------------------------------gtaatttatctttgcct--tgatctagtttattgcacatt----ctttgattcttatttatcatcattcatgatgattatcaaattgctgtat---tgttttcagATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCTATACTGGTGATTCAGCAAGAAGAATATGGGACGCTATTTACAAAGAGAA
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 3
gtaacttttctttacagtctacttcatttttgattcttacatgtcgaaactctatcgctacttcatatataactggctcatgagatgatatgtaacaa-gtaggggttttagcatcgaattgctat-gtgttagatgcagtttttgatgactgtatatatgatcgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
||| | || |||| | | | | | ||| || ||| | | || | | | | || |||| || | ||||||| ||||| || || ||||||| || ||||||||||| ||||||||||||| || ||||| || ||||||||||| ||||| || |||||
--------------------------------------------------------------------gtaatttatctttgccttgatctattctattgcacattctttgtttcttgtttattatcattcttgacg-attatcaaattgttgtac---tgttttcagATGAGATGACTTACGTGAATCTTCAACTGAATCCTGAACGATACACTGGCTATACCGGTGATTCAGCAAGGAGGATATGGGATGCTATTTATAAAGAGAA
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 3
gtaacttttctttacagtctacttcatttttgattcttacatgtcgaaactctatcgctacttcatatataactggctcatgagatgatatgtaacaagtaggggtttta-gcatcgaattgctatgtgttagatgcagtttttgatgactgtatatatgatcgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
||||| || | ||| |||| | | || | | | | || ||||| || | | | | | | ||||| | || | |||||||| |||||||| || ||||||| || ||||| ||| | || ||||| |||| ||| |||||||| |||||||||||||| ||| | ||||| |||||
--------------------------------------------------------tttactttttacactgttggtgtatgaaa--------attaaatcattttctaatatattgaatttctttccaagaaaaataagcat-gtcaactgtttgcat--ttgcagATGAGATGACATACGTGAATCTTCAACTGAATCCCGAAAGATATACTGGTTATACTGGTCCATCAGCAAGAAGGATATGGGATGCTGTCTACTCAGAGAA
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 3
gtaacttttctttacagtctacttcatttttgattcttacatgtcgaaactctatcgctacttcatatataactggctcatgagatgatatgtaacaagtaggggttttagcatcgaattgctatgtgttagatgcagtttttgatgactgtatatatgat-cgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
|| || | || | || | | | | || || ||| | ||||| | || | | | | | | | |||| |||||||| |||||||| || ||||||| || ||||| ||| | || ||||| || | ||| ||||| || |||||||||||||| ||| | |||||||||||
------------------------------------------------------------------atttactttttacact-gttggtgtatgaaaattaaatcattttataataaattgaacttctttccaagaaaaataagcatgtcaactgtttgatatgcagATGAGATGACATACGTGAATCTTCAACTGAATCCGGAAAGATATACTGGTTACACTGGTCCATCTGCAAGAAGGATATGGGATGCTGTCTACTCTGAGAA
upper sequence: AT2G38960.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 3
gtaacttttctttacagtctacttcatttttgattcttacatgtcgaaactctatcgctacttcatatataac-tggctcatgagatgatatgtaacaagtaggggttttagcatcgaattgctatgt--gttagatgcagtttttgatgactgtatatatgatcgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
|| || | ||| | || | | || || || | | | || || | ||| || || |||||||| | || | | |||| || ||||||||||| ||||||| || || |||||||| |||||||| |||| ||| ||||| || ||||||||||||| ||||| || |||||||
------------------------------------------------------------------caatgacattgcttagtcaataacactc--catgtttcttttcttttcttaagtttctttaatggtttaataaagcttttgatggtt-cattttcatttgcagCGGAGATGACATATGTGAATCTTCAACTGAACCCTGAACGCTACACTGGATATACTGGTCCATCTGCACGAAGGATATGGGATGCTATTTATACTGAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcgaattgctatgtgttagatgcagtttttgatgactgtatatatgatcgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
ttttgat putative branch site (score: 4)
tatatatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttttctttacagtctacttcatttttgattcttacatgtcgaaactctatcgctacttcatatataactggctcatgagatgatatgtaacaagtaggggttttagcatcgaattgctatgtgttagatgcagtttttgatgactgtatatatgatcgcagATGAAATGACATATGTTAATCTTCGGCTTAATCCTGAACGGTACACTGGCTATATTGGCCCATCAGCTAGAAGGATATGGGAAGCTATATACTCTGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT