Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcatgtctcctactgctttttagttttttatcctctgtggctcatgtttgatacaaatttcaactgttttcagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51150.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 2
--------------------gtaaggcatgtctcctactgctttttagttttttatcctctgtggctcatgtttgatacaaatttcaactgtttt----cagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA
| || | | ||||| ||| | | ||||| | | || | || || || |||| || | || || |||||||||||||||||||| ||||| ||||| |||| || || || || ||| | || || ||||| ||||| || ||
gtaagcaccgaagaaatgacgcaacttcgttgcattgtcgctttgagttttgtgaggtgatgtggggtaactaacatctgcacttgggttggttcttggcagCAAGCATATTCGCGTATGGGCAAACAAGCAGTGGCAAGACTTACACGATGACCGGGATAACCGAGTATAGTGTTCTCGACATCTATGACTACATCGAAAA
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 2
--------------------------------gtaaggcatgtc-tcctactgctttttagttttttatcctctgtggctcatgtttgatacaaatttcaactgttt--tcagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA
| | || || | | | | | || || | | || || | | | || || || ||||| || | ||||||||||| |||||||||||||| ||||||||||| |||| ||| || || || || | || | || || | | | ||||| || ||
gtgagtttcttctctttgtctgcttttcctccttcatcagcatcatcaaaatccacgtaatttccttgttaacatcttcttttgatctctccccatggtgtctaattgatcagCAAGCATTTTTGCATATGGACAAACAAGCAGTGGGAAGACATACACCATGAGTGGCATAACTGAATACACAGTGTCAGACATTTTTAACTACATAGAAAA
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G07950.1 (Glycine max), 3'ss of exon 2
-----------------------------------gtaaggcatgtct---cctactgctttttagttttttatcctctgtggctcatgtttgatacaaatttcaactgttttcagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA
| || || | || | || || || | | ||| | || | | | | || | | | ||||| || | ||||||||||| |||||||| ||||| ||||||||||| |||| ||| || || || || | |||| || || | | | |||||||| ||
gtgagtttcttccctttctatgcttttcctccttcatcagcatcatcaaaatccacggaacttctgtgtt--aacgtcttcttttgatctctccccctggtgtctaat-tgatcagCAAGCATTTTTGCATATGGACAAACAAGTAGTGGGAAGACATACACCATGAGTGGCATAACTGAATACACAGTGGCAGACATTTTTAACTACATTGAAAA
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G24250.1 (Glycine max), 3'ss of exon 2
------------------gtaagg-catgtctcctactgctttttagttttttatcctctgtggctcatgtttgatacaaatttcaactgttt--tcagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA
|||| | ||| | ||| || || | | || | | | |||||| || | || ||| ||||| || | ||||| ||||| ||||||||||| ||||| |||||||| |||| |||||| || |||| |||| | || ||||| | | ||||| || ||
gtgagtttttcttccttcataagaatgaatgtccaaggaatttctatattaacaacttcggccgggccaatttgatctttgatt-acctatttgatcagCAAGCATTTTTGCTTATGGACAAACAAGCAGCGGAAAAACATACACCATGAGTGGTATAACAGATTTTGCCATAGCAGATATTTTCAACTACATAGAAAA
upper sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 2
----gta-aggcatgtctcctactgc------tttttagttttttatcctctgtggctcatgtttgatacaaatttca----actgttttcagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA
||| | ||| | | | || || | || || | | || | | | | |||||| | | | | | ||| |||| ||| | ||||| ||||| |||||||||||||||||||||| |||||||| || ||||| || ||| || |||| ||||||||||| | || ||||
gtgagtataaacatttttttttttgtgtccttttcctgcttcttgaacttcacttggacctcattgataaatactcaacaaaatattttccagCAAGTATTTTTGCTTATGGACAAACAAGCAGTGGAAAGACATTCACTATGAGCGGAATTACTGAGTATACCATGGCAGATATATATGACCATATAGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagttttttatcctctgtggctcatgtttgatacaaatttcaactgttttcagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA
gtttgat putative branch site (score: 5)
ctgttttc putative PPT
tttgatacaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcatgtctcctactgctttttagttttttatcctctgtggctcatgtttgatacaaatttcaactgttttcagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT