Sequence
atgc intronic sequence ATGC exonic sequencegtaccttccttcaaatatctatagactcagttcaatacatcttagatgattgtgaagtggtaaaaggttaaacttagttagttctatgcacctaactagaatgtttttttttaaaacaaaccttaaccagaatctggatgtaaatggtaatcatatgatatacactaaatatgattcttggtgaattgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32430.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g38050.1 (Oryza sativa), 3'ss of exon 10
gtaccttccttcaaatatctatagactcagttcaatacatcttagatgattgtgaagtggtaaaaggttaaacttagttagttctatgcacctaactagaatgtttttttttaaaacaaaccttaaccagaatctggatgtaaatggtaatcatatgatatacactaaatatgattcttggtgaattgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA
| | || | | | |||||| || ||| | | || | | | | || || | | | | | | || ||| ||| | | ||||||||| ||||||||||| || ||||||||| | || | || || |||||||||| || ||||| ||||||| ||| || |||||||| || ||||| ||
---------------------------------------------------------------------------------tgatgaaatttcaaatc-atttttttttcttttgtcaacttctgatcatattttagcc--aactgttggttacaaatttttcaa-----atggttcgcact--actgcagATTGCGAATGGAAGGCGCAGGCAGGCAACGTGTGCGCCGCGTCGTTCGACTGGAGCTGCAGCGGCATCTGCAAATCGGCGGATCGGATGAAGGAGGTCCA
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 10
gtaccttccttcaaatatctatagactcagttcaatacatcttagatgattgtgaagtggtaaaaggttaaacttagttagttctatgcacctaactagaatgtttttttttaaaacaaaccttaaccagaatctggatgtaaat-ggtaatcatatgatatacactaaatatgattcttggtga--attgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA
|| | | || | || | | | | || | | | || ||| || | ||| | | || |||| ||||| | ||||||||||||||||||| ||||||||||||||| | ||||| |||||||| || |||||||| || || || ||||| || ||||| |||| |||||||||||
-------------------------------------------------------------------------------------------atagtttagcttttatattatcacatcattatttatttgg-tttgtttgtttattagcaatggt-caacattt-tgaaattcttgagttggtcatgcttgcagATTGTGAATGGAAAGCACAAGCAGGCAACGTTTGTGTTGCTTCATTTGATTGGACGTGCAGTGGAATTTGCAGGTCTGCTGAAAGGATCAAAGAGGTTCA
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 10
gtaccttccttcaaatatctatagactcagttcaatacatcttagatgattgtgaagtggtaaaaggttaaacttagttagttctatgcacctaactagaatgtttttttttaaaacaaaccttaaccag--aatctggatgtaaatggtaatcatatgatatacactaaatatgattcttggtgaattgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA
|| | | | | | ||| | || | | | || | || || |||| || | | ||| || | | | | || | || || |||||||||||||||| ||||| |||||||| | ||||| |||||||| || |||||||| ||||| || ||||| || ||||| |||| |||||||||||
-----------------------------------------------------------------------------------ctttttatattatcacaatatcacttcattattta---tttggtttgtttatttgttagtaattgtctacattttgaaattc-ttgagt-tggtaattc-----tttcagATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGTGTTGCTTCATTTGATTGGACGTGCAGCGGAATTTGCAGGTCTGCTGAAAGGATCAAAGAGGTTCA
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 10
gtaccttccttcaaatatctatagactcagttcaatacatcttagatgattgtgaagtggtaaaaggttaaacttagttagttctatgcacctaactagaatgtttttttttaaaacaaaccttaaccag--aatctggatgtaaatggtaatcatatgatatacactaaatatgattcttggtgaattgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA
|| || | | ||| | | | | || ||||| | | | || | |||| | || | || || | |||| || || || ||||||||||||| |||||||||||||| || ||||| ||||| || ||||| || |||| || || || || ||||| || ||||| |||| |||||||| ||
-----------------------------------------------------------------------------------gtaaatacttttcctaaatatataaatcatattgaatccttatctgtttagtttgtttacaaattattattaattgttaaattgcaaat-tggttattc-----ttgcagATTGTGAGTGGAAGGCACAAGCTGGAAACATTTGTGTTGCATCATTTGATTGGAGCTGCAGTGGAATTTGCAGGTCTGCTGAGAGGATTAAAGAGGTACA
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G46230.2 (Glycine max), 3'ss of exon 10
gtaccttccttcaaatatctatagactcagttcaatacatcttagatgattgtgaagtggtaaaaggttaaacttagt---tagttctatgcacctaactagaatgtttttttttaaaacaaaccttaaccag---aatctggatgtaaatggtaatcatatgatatacacta-aatatgattcttggtgaattgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA
||||| || || | | || || | || | | |||| || | | | || ||| | | | | | || | || | | || | || || ||| | || || || || | ||||||||||||| |||||||| |||||||| ||||| ||||| || ||||| || |||| || || || || ||||| || ||||| |||| |||||||| ||
-----------------------------------------------------------gtaaatacttttcctgaatatataaatcacagtgactcatttaaatgattgatgt--gatcataccattatctgtttggtttgtttacaacttattattaattgtta-acattgcaaattggttattattc--ttgcagATTGTGAGTGGAAGGCCCAAGCAGGGAACATTTGTGTTGCATCATTTGATTGGAGCTGCAGTGGAATTTGCAGGTCTGCTGAGAGGATTAAAGAGGTACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgtaaatggtaatcatatgatatacactaaatatgattcttggtgaattgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA
cactaaa putative branch site (score: 2)
taatcatatgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccttccttcaaatatctatagactcagttcaatacatcttagatgattgtgaagtggtaaaaggttaaacttagttagttctatgcacctaactagaatgtttttttttaaaacaaaccttaaccagaatctggatgtaaatggtaatcatatgatatacactaaatatgattcttggtgaattgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG