Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttatcacacggagcttgagtttctgagttaagtgaatgtacctgaacaaatgcttctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30910.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G178958_T01 (Zea mays), 3'ss of exon 5
-----------------gtaagtttatcacacggagcttgagtttctgagttaagtgaatgtacctgaacaa-----atgcttctttgcacaatt---agGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
| | | || | ||| || | | | | | | || ||| || ||| || ||| | | | |||| |||||||| ||||| || ||||| |||||||| ||||| || || ||||||||||| || | | || || || || |||||||||||||||
gtacttcatttttcacagccgcctagctgtatagatgtagaggtttt-acccatattagtttatctgttaaatttctatgtttttttccccttctcacagGTTCACTTTATAGTCGCTGCCTGTGAAAATATGATCAGTGGCACAGGCATGAGACCTGGTGACATTGTAACTGCTTCCAATGGGAAGACAATTGAG
upper sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G028114_T01 (Zea mays), 3'ss of exon 9
-----------------gtaagtttatcacacggagcttgagtttctgagttaagtgaatgtacctg---aacaaatgcttctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
| | | || | ||| || | | || | | | || ||| | ||| || | | |||| |||||||| ||||| || ||||| |||||||| ||||| || || ||||||||||| || | | || || || || |||||||||||||||
gtacttcatttttcacagccgcctagctgtatagatgtagaggtttt-acccaaattagtttatctgttaattctatgtttttcccttctcacagGTTCACTTTATAGTCGCTGCCTGTGAAAATATGATCAGTGGCACAGGCATGAGACCTGGTGACATTGTAACTGCTTCCAATGGGAAGACAATTGAG
upper sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G08150.1 (Glycine max), 3'ss of exon 5
----gtaagttta----tcacacggagcttgagt------ttctg-agttaagtgaatgtacctgaacaaatgctt----------ctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
| ||||| || | |||| ||| || || || || ||| | || | ||||| | || |||| || |||||||| |||||||||||||||||||||||||| || || ||||| ||||||||| | ||||||| ||||| || ||||| || |||
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtagtaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
upper sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 5
--------------gtaagtttat-cacacggagcttgagtt----tctgagttaagtgaatgtacctga-acaaatgctt-----ctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
|| | || | | | | | ||| | | | | |||| | || | | | || | |||| |||| || ||||| || |||||||||||||||||||||||||| || || ||||| ||||||||| | ||||||| ||||| || ||||| || |||
gcatatgttgttgaataggattgtgcttatagcttctttgttcatctttttgcacaaaaaatgcatcttatatcccagtttaaaaaccctgcatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
upper sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 5
---------gtaagttta----tcacacggagcttgagt------ttctgagttaa-----gtgaatg---tacctgaacaaatgcttctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
| ||||| || | ||| ||| || || || | ||| || ||| |||| | || | || || |||| || ||||| || |||||||||||||||||||||||||| || || ||||| ||||||||| | ||||||| ||||| || ||||| || |||
tggtggctaatttgtttagagttctgatggatattgtgtagtatcttttgtggtaataataatgcatgcaatacccagattaaaaatcct--acatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
upper sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 5
----gtaagttta----tcacacggagcttgagt------ttctgagttaagtgaatgtacctgaaca-aatgctt----------ctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
| ||||| || | |||| ||| || || || | | | |||| || | ||||| | || |||| || |||||||| ||| | |||||||||||||||||||| || | ||||| ||||||||| | ||||| | ||||| || ||||| || |||
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
upper sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------------------gtaagtttatcacacggagcttgagtttctgagttaagtgaatgtacctgaacaaatgcttct-ttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
||| ||| | || || ||| | || | ||| | | | ||| | ||||||| || ||||| |||||||||||||||||||||||||| || || ||||| |||||||| || ||||||| ||||| || ||||||||||||
gtaagccagttgttgttgttgttgttatcattgtttgtttgttttaacttgcatggaacaatttcttaactaatccatttgtatgttctattttcaattctccagcaattgaatctagcatacacttatgacttattaagggtcttgtatttgcagGTGCATTTCATTGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGCATGAGGCCTGGAGACGTTGTCACAGCTTCAAATGGAAAGACAATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgagtttctgagttaagtgaatgtacctgaacaaatgcttctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
cttctttgc CT-rich tract
aacaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttatcacacggagcttgagtttctgagttaagtgaatgtacctgaacaaatgcttctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA