Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaagccattttttctttcacttttagcatctcttaatagtctgttttttggcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03000.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os04g52690.3 (Oryza sativa), 3'ss of exon 9
------------------------------------gtaagtaagccattttttctttcacttttagcatctcttaatag----tctgttttttg---------gcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
| ||| | | || | || | || ||||| | | || | | | | | | | | | | | || || ||||| ||||| ||| ||||||||||||| || ||||||||||| ||||| || || |||||||| ||||||||||| || ||||||||| ||||||| || ||||| |
gttggtttacggtgtttttctattttatactttgtttttagttaagctttaccttttcgtttcttcccatctgtccaaagaggataagcacatagaaaagcactgtatacgtgctcattattattatgtttcaatttgcagACATTATTGGCAAAAGCTGTAGCAACAGAGTGCTCTTTAAACTTTCTTAGTGTAAAAGGTCCAGAATTGATTAACATGTATGTTGGAGAATCGGAGAAGA
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 9
------------------gtaagtaagccattttttctttcacttttagcatctcttaatagtctgttttttggcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
|||| | | | || || | ||| || | | | ||| | | || | ||||| | | || ||| ||| |||||| ||| | ||||||||||| || |||||||||||||||||||| || ||||| || ||||| ||| | ||||||||||| ||||||||||| || || |
gtaagttgtaatgtaactgtaaatga-caatgttctacctcatttgtctaacgttttacttaaaaaaatatttctaacaccattttcttgctcttttatttaata-acagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G36930.1 (Glycine max), 3'ss of exon 14
------------------------gtaagtaagccattttttctttcacttttagcatctct-taatagtctgttttttggcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAA--GCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA-----------------------
|||| | | | || | | ||| || | | | | | || | ||| || || ||| | | | ||| | |||| ||||||| ||| | |||||| ||||| || ||| |||| ||||||||||| || || || || ||||| ||| | ||||||||||| ||||||||||| || || |
gtgatctggtgttcttttgtacctgtaaatga-caatgctctacctcatttctgttacttttatcttaaaaagatttaaaaca-ccat-tttctcactcttttatttaa---tacagacattattagcaaaaaagctgttgctacatagtgttccttaaattttcttagCGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGAATGTTCGAGACATTTTCCAGAAG
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 9
----------gtaagtaagccattttt-------tctt------tcacttttagcatctcttaatagtctgttttttggca-gttatatttttgagtttttgaatta-aatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
|| || ||||| || | ||| | | || | | | | || || | | ||| || || ||| | | ||| || | ||||||||| ||||||||||||| || |||||||||||| | ||||| || |||||||| || || ||| | |||||||||||||| ||||| ||||||||||
gtaagtttttgtttgttagccacttatggtgatatctcaatacgttatttcttgtttatttttttaaccaggaacctggttcattgctttcttggttactcctattgcaaatctcagACTTTATTGGCAAAAGCTGTTGCAACAGAGTGCTCCCTCAATTTTCTGAGTGTAAAAGGGCCTGAACTGATCAACATGTATATAGGAGAATCAGAGAAAA
upper sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------gtaagtaagccatttttt---ctttc-----acttttagcatctcttaatagtctgttttttggcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
| || ||| | | || | | || | | | | || || || | ||| || | | || || | || || ||||| || || || || ||||| || || |||||| | || || || || ||||| || ||||| || | ||||||||||| ||||||||||||||||| |
gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaaca-ctaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatagtctgttttttggcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
tcttaat putative branch site (score: 3)
agttatatttttgagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaagccattttttctttcacttttagcatctcttaatagtctgttttttggcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA