Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctctgtactacaattttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59110.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 4
-----------------gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctctgtactacaattt---tacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
|| || |||| | ||||| | |||| | ||| | | | | |||| | ||| ||| || || |||| |||||||||||||||||||||||||||||||| |||||||| || ||| | || || ||| ||||||| || || || || || || ||||||| || ||||||
gtaagaaacaaaccatcgtcc-ccgtcaaaaagaaaagaattgttcttcactttagctc---ttttatatgtatatgtttagttgcataacc-cattttccataactgaattggtatacagGCTTGCTTATTTACATGAAGCAATAGAGCCAAAAGTTGTACACCGGGATATCAAATCAAGCAACATACTAATCGATGAAGAATTCAATGGCAAACTTTCT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g44110.1 (Oryza sativa), 3'ss of exon 5
gtaagttgtttaaaatgtgactgttgttgga--ccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctctgtactacaattttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
||||||| | | | | | || | | || || | || || | ||| | | || ||| | | | | | || |||| || ||||| | |||||||| |||||||||||||| || ||| |||| |||||| ||||||||||| ||||||| || || || |||| ||| | |||
gtaagtttcatcagcttctcagtctataagatacatgttgtttctgttgtcggaatt---tgtttgatgatattttggcgggtta---atcatgatc--acagACTAGCTTACCTTCATGAAGCTATAGAACCAAAAGTTGTGCACCGAGATATAAAATCAAGCAATATCTTGATTGATGAGGAATTTAATGGCAAGGTCTCT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 4
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctctgtactacaattttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
||||| | | || | | || || || |||| | | | | ||||| ||| || | | || | |||||||||||||||||||||||||| |||||||||||||| || ||| | || || ||| | ||||||||||| |||| || || ||||||| |||||||||
gtaagacatggaccattcaa----tattttgtctcttctttgatgcat-atgttttgccatctaagg---catttttataattgatgatata---ctacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTGCACCGTGATATCAAATCTAGCAATATCCTAGTTGATGAAGAATTCAATGGCAAGCTTTCT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 2
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctctgtactacaattttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
||||| | || | || || ||| | |||||| || | | | | ||||| | | | ||| || |||| |||||||||||||||||||||||||| |||||||||||||| || ||| | || || ||| | ||||||||| | ||||| || || ||||||| |||||||||
gtaagaaatgaaaccattcacaatt-ttgcatcttttatatgca----tacatttattaaattaagatgttgtctaca-actgaacacta------tacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTACACCGTGATATCAAATCGAGCAATATCTTAATTGATGAAGAATTCAATGGCAAGCTTTCT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 5
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctc--tgtactacaatt--ttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
|| || |||| || || | | |||| | ||| ||||| | ||| | ||| || | |||||| | | | ||||||||||||||||||||||||||||||||||||||| | ||| | || ||||| | ||||| || ||||||||||||| |||||||||||| |||||
atattttacttaattagttacaaattta-----tttttatggaagattcaacgatggaacttgttctgctaattaacccccctaatgtactgtgactggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGACGATGAATTCAATGCAAAGGTTTCT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctc-tgtactacaatt--ttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
||| | ||| | | || || | | | | || ||||| | ||| ||| || | |||||| ||| | ||||||||||||||||||||||||||||||||||||||| | ||| | || ||||| | ||||| || ||||||| ||||| |||||||||||| |||||
-ccagtagcttagagtagcttagtcgtctgttcgtgt---caaagattcaatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactct--ttaaggggatattgacatgctctgtactacaatt--ttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
| | | | | || | || || ||| | | | |||||| | | || || ||| | || | | ||||| | | | |||||| ||||| |||||||||||||||||||| ||||| || ||| | || ||||| ||||||| || ||||||| ||| |||||||||||| |||||
-tgtgcttgcttcattggatacctaattta--ctgtta-tggcagtttcaacattaggcctaattccactgat-taaactccttatttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactct--ttaaggggatattgacatgctctgtactacaatt--ttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT-
|| | || | | || | | || ||| | | | |||||| | | || || ||| | || | | ||||| | | | |||||| ||||| |||||||||||||||||||| ||||| || ||| | || ||||| | ||||| || ||||||| ||| |||||||||||| |||||
gtgcttgcttcactggatacctaattta----ctgtta-tggcagtttcaacattaggcctaattccactgat-taaactccttatttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
upper sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttgtttaaaa-tgtgactgttgttggaccttttacttgaaatttcaaaaa--caactctttaaggggatattgacatgctctgtactacaattttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
|| || | || || | || || | | | || | || || || | | | ||| | || | || ||||||||| ||||| ||||| ||||||||||| ||||| || || ||||||||||| ||||||| ||| ||||||| ||||| |||||||||||| |||||
-tattccattcagaactgaaatctactccagaactgaaattgaacatcttggtctttcacactttgaaaaagtcaaaaaaatgtttcatattggg---ttgcagGCTTGCCTATTTGCATGAGGCAATAGAACCGAAAGTTGTTCATCGAGACATAAAATCAAGCAACATCTTGATTGATGATGAGTTCAATGCAAAGGTTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaaaaacaactctttaaggggatattgacatgctctgtactacaattttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
tattgac putative branch site (score: 2)
tacaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctctgtactacaattttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG