Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatacacaatatacaatataattcaaaaattacatagtttttgtttgtaacagttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26590.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g38400.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------gtatgtatacacaatata-caatataattcaaaaattacat--agtttttgtttgtaacagttacattatttatctgt---catgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
| | || ||| | | | | | | | | | || ||| | | | | | ||| | ||| | || || |||||||||| ||||| || | ||||| || | || ||||||||||||||||||||||||||| |||| | || || || || ||||| ||
gtacatacatgtgacttcgactgacacctgacaaattgtgtcctgaaaattgtttccatgttctagttggaagtactgattttcaggttcataatctttctgtgttgctggtttgctgtcttaatctcttttttcttttggctctaatctttctgtgtttgtgggcagCTGATGGGATATGGTTGGGCTGGCCTCTTCAGAAAGTTTCTTGTGGACTCACCTTACATGTGGTGGCCTTCAAACTTGGTACAGGTTTCACTCTTCAG
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g23130.3 (Oryza sativa), 3'ss of exon 3
----------------gtatgtatacacaatatacaatataattcaaaaattacatagtttttgtttgtaaca-gttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
| || || | | | | | | || ||| | | || | || | | |||||| | |||| ||||| | || ||||||||||| || |||||||||| ||||| || |||||| | |||||||||||||| |||| || || |||||| | ||||| ||
gttgccactcatgcattggttgattagtaacaaatcgaagacctgatcaaacacacattgattaatccaaaaatggccttttatttgatt-tcatacagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G47140.1 (Glycine max), 3'ss of exon 1
-------gtatgtatacacaatatacaatataattcaaaaattacatagtttttgtttgtaa---cagttacattatttatctgtcatgt---------agTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
|| | | | ||| ||| | | | | | || ||| || |||| ||| | | | || || || || | || ||||||||||| || || ||||||| || ||| ||||| || || ||||||||||||||| |||| ||||| ||||| ||||| || ||
acttctcccat-cacagatgcctcctaatcctattaatcatcaaaagaacttgcattttcaaatatggttagtttactaaaccgtgtcgttgaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G01610.1 (Glycine max), 3'ss of exon 4
-------gtatgtatacacaatatacaat-ataattcaaaaattacatagtttttgtttgtaacagttacat-tatttatctgt---------catgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
| | | | | |||||| | |||| | | || | | | | | || | | | || | | | | || | ||| || | || ||||||||||| || || |||||||||| || || || || || ||||||||||||||| |||| ||||| ||||| ||||| || ||
ggaatccacttttctttgtattttacaatcaaaatttctataatagaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatgtttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0015g00860.t01 (Vitis vinifera), 3'ss of exon 2
-------------gtatgtataca--caatatacaatataattcaaaaattacatagtttttgtttg---taacagttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
|| |||| ||| || | ||||| | | || | | ||||| | | |||| | | || | | || ||||| | || ||||||||||| || ||||||| ||||||||||||||||| || || ||||||||||| ||||||| || |||||||||||||| ||
tgtagtatatggtttactcatactactaatccaccaattaatttgatattttagtttctcttgttcaccttgatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
----------------gtatgtatacacaatatacaatataattcaaaaattacatagtttttgtttg---taacagttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
||| ||||| | || | ||||| | | || || | ||||| | | |||| | | || | | || ||||| | || ||||||||||| || ||||||| ||||||||||||||||| || || ||||||||||| ||||||| || |||||||||||||| ||
atatattacttattttgta-gtatatggtttccaccaattaatttgatattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0015g00890.t01 (Vitis vinifera), 3'ss of exon 1
---------------gtatgtatacacaatatacaatataattcaaaaattacatagtttttgtt---tgtaacagttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCT-TACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
||| | ||||| | ||||||| | | ||| | | || | ||| |||| | | || | | || ||||| | || ||||||||||| || ||||||| ||||||||||||||||| || || ||||||||||| |||||| | || |||||||||||||| ||
cctactgcttattttctattttctgcttatatatcaatcaattcaatatattaatatctctcattaactataatagtttcccttcttctgttgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCCTATATGTGGTGGCCAGCAAATATGGTCCAAGTCTCTCTCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaaaattacatagtttttgtttgtaacagttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
ttgtaac putative branch site (score: 2)
tttatct putative PPT
aattacatagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatacacaatatacaatataattcaaaaattacatagtttttgtttgtaacagttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG