Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttaagacctctacaaatttttcattttgtaaagttttggttttgttaattgcttttggattgtgtcggtgttttaagCACATATCTGGTGAGACTGTTGGAGAGGTAAGAATTGTTTCAGACATGCACGAGCGCAAAGCTACAATGGCTCAAGAAGCTGGGGCTTTCATTGCGCTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 3
---------------gtatgtttaagacctctacaaatttttcattttgtaaagttttggttttgttaattgcttttggattgtg--tcggtgttttaagCACATATCTGGTGAGACTGTTGGAGAGGTAAGAATTGTTTCAGACATGCACGAGCGCAAAGCTACAATGGCTCAAGAAGCTGGGGCTTTCATTGCGCTCC---
|| | | || | || ||||| | | ||| | | | | | ||||||| | | || | | | ||| || ||||||||||| | ||||| || ||||||||||||||||| ||||| ||||| |||||| |||||||||||||||||| || || || || ||||
gatagtagtccctttgt-tatgaaaaaaaattatggtgctttcaatgtcgaaaatat--gatcttttaattgttagtaagttataatttgcctattttgacagATATCTGGTGAACCAGTTGGTGAAGTAAGAATTGTTTCAGATATGCATGAGCGTAAAGCTGCAATGGCTCAAGAAGCTGATGCATTTATCGCCCTCCCTG
upper sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 3
-----------gtatgtttaagacctct---acaaatttttcattttgtaaagttttggttttgttaattgcttttggattgtgtcggtgttttaagCACATATCTGGTGAGACTGTTGGAGAGGTAAGAATTGTTTCAGACATGCACGAGCGCAAAGCTACAATGGCTCAAGAAGCTGGGGCTTTCATTGCGCTCC---
| || | | |||| || || | |||| | | ||| | | || | | | | ||| || ||||| ||||| || || || || || |||||||||||||| ||||||||||| |||||| | |||||||||||||||| || || |||| ||||
atggttgttctttttgataatgacccctttgccatggaaataatttctagatgcttttgatggagaaaatatgatcactgaattcttgcaattttgacagATATCAGGTGAAACAGTAGGTGAAGTGAGAATTGTTTCAGATATGCACGAGCGTAAAGCTGCCATGGCTCAAGAAGCTGATGCATTTGTTGCTCTCCCTG
upper sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G11070.1 (Glycine max), 3'ss of exon 3
------------gtatgtttaagacctctacaaatttttcattttgtaaagttttgg-ttttgttaattgcttttggattgtg--tcggtgttttaagCACATATCTGGTGAGACTGTTGGAGAGGTAAGAATTGTTTCAGACATGCACGAGCGCAAAGCTACAATGGCTCAAGAAGCTGGGGCTTTCATTGCGCTCC---
||| || | | || ||||| | || ||| | | |||| | |||||| | |||| | | ||| || ||||||||||| | ||||| || ||||||||||||||||| ||||| |||| |||||| |||||||||||| ||||| || || ||||| ||||
gtagtccctttgtcatgaaaaaaaaat-tatggtgctttcaatgtggaaaatatgatcttttaatttttgcttgtaagttgtaatttgtctattttgacagATATCTGGTGAACCAGTTGGTGAAGTAAGAATTGTTTCAGATATGCATGAGCCTAAAGCTGCAATGGCTCAAGGAGCTGATGCATTTATTGCTCTCCCAG
upper sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 3
---------------gtatgtttaagacctctacaaatttttcattttgtaaa-gttttggttttgttaattgcttttggattgtgtcggtgttttaagCACATATCTGGTGAGACTGTTGGAGAGGTAAGAATTGTTTCAGACATGCACGAGCGCAAAGCTACAATGGCTCAAGAAGCTGGGGCTTTCATTGCGCTCC---
||| | | ||| | | | | ||| || | | |||| | | ||| | | ||| | |||| | || ||||||||||| || || || || || || ||||||||||| ||||||||||| || ||| ||||||| |||||||||| || || |||| ||||
tatggttgttcttttttataat-gacccctttgccatggaaataatttatagatgctttgatggagaaaatatgatcagtgaattgttgtaattttga-cagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG
upper sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 3
-------gtatgtttaagacctctacaaatttttcattt-tgtaaagttttggttttgttaattgcttttggattgtgtcggtgttttaag-
|||| | | | || ||| || | | | || | | | | | || | ||||| || | || || |||||||| | ||||||||||| ||||||||||| || |||||||| ||||| |||||| ||||||||||||||||| ||||| ||||| || |
tagttccctatgatggaaagtacttcaatcttgtgagcagcttggagcatgtgaacaatggactactaatatattgttaacatgggtaaaatggtgacagATATCTGGCCAAACTGTTGGAGAAGTAAGAATTGTGTCGGACATGCATGAGCGGAAAGCTGAAATGGCTCAAGAAGCTGATGCTTTTATTGCTCTTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgtaaagttttggttttgttaattgcttttggattgtgtcggtgttttaagCACATATCTGGTGAGACTGTTGGAGAGGTAAGAATTGTTTCAGACATGCACGAGCGCAAAGCTACAATGGCTCAAGAAGCTGGGGCTTTCATTGCGCTCC
tgttaat putative branch site (score: 3)
ttttgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttaagacctctacaaatttttcattttgtaaagttttggttttgttaattgcttttggattgtgtcggtgttttaagCACATATCTGGTGAGACTGTTGGAGAGGTAAGAATTGTTTCAGACATGCACGAGCGCAAAGCTACAATGGCTCAAGAAGCTGGGGCTTTCATTGCGCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG