Sequence
atgc intronic sequence ATGC exonic sequencegtacttcaaaacacttttaacatattaagatatggaaaaaagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08020.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 3'ss of exon 9
-----------------------gtacttcaaaacacttttaacatattaagatatggaaaa-----aagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
| | | || | || | | ||| ||| | | ||| || | ||| | ||||||||||| |||||||| | || || || ||| | |||||||| |||||||| ||||||||||| |||||||||||||| |||||||| || ||||| |
gtaaaatcttggaatctttgaaagaaaatggaattgttcttgatgt-ttagtttattagcactttctagttgtgattgtcctaaatttacttgttatgttttgcagCCTGTGTTCTTCAGTCTGAATGCCTATATTAGCCTTATCAAGCCTGACCAAACCATGTGGTACCGAGCTTGCAAGACCTGCAACAAGAAGGTGACTGAGG
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G098714_T01 (Zea mays), 3'ss of exon 9
---------------------gtact-tcaaaacacttttaacat--attaagatatggaaaa----aagaaaagttgatttatgagtctcgtatat-atattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
| || | | | | || || | | ||| | | || | ||| |||| |||| | | | | | |||||||||||| |||||||| || ||||||| ||||||||| ||||| | |||||||||||||||||||||||||| |||||||| || ||||||
gtataatcgtcaatatccactgaacgatgatattatttatatcttgaattgaaaaattgtaaatttggagaacccccaatttgacccttttatttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G086934_T01 (Zea mays), 3'ss of exon 9
-------------------gtacttcaaaacacttttaacatatt------aagatatggaaaa--aagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
| | ||||| || || || |||| || ||| || | | || ||| || | | ||||||||||| |||||||| || ||||||| ||||||||| || || | ||||||||||||||||||| ||||||||||||||| || |||||||
gtacgatcctgaatattcactgaaatatgacactgttcgtatctttaatggaagaattgcaaatctggagaagctccaattcgacttcttgtttttcccttgcagCCTGTTTTCTTCAGTCTGTACGCCATCATAAGCCACATCAAGCCTGATCAGAATATGTGGTACCGTGCTTGCACGACCTGTAACAAGAAGGTGACTGAAG
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G468475_T01 (Zea mays), 3'ss of exon 8
----------------gtacttcaa-aacacttttaacatatt------aagatatggaaa---aaagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
||| || |||||| || || || |||| || ||| |||| ||| | | | | | ||||||||||| |||||||| || ||||||| ||||||||| || || | ||||||||||||||||||| |||||| |||||||| || |||||||
gtacgaccctgaatattcactaaaataacactgttcgtatcttcaatggaagagttgcaaatctggagaagctccaattcaacttcttgttttttcctttgcagCCTGTTTTCTTCAGTCTGTACGCCATCATAAGCCACATCAAGCCTGATCAGATTATGTGGTACCGTGCTTGCATGACCTGCAACAAGAAGGTGACTGAAG
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------------------gtacttcaaaacacttttaacatattaa--gatatggaaaaaagaaaagttgatttatgagtctcgtatatatatt---gcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
| | | ||| ||| || || | || ||| | | | |||| | | |||||| ||| | || |||||| | ||| ||||| ||||| | ||||||||||| ||||| || || |||||||||| ||||| || ||||| || || |||||||||||||||
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaa-atttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------gtact-tcaaaacacttttaac----atattaagatatggaaaaaagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
| ||||| | ||| | | ||||| || | || ||||| | || || | | ||| ||||| ||| || |||| ||||| |||||||||||||||||||| || |||||||||||||||| ||||| ||||| || ||||||||||| || || |
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaatcattttaagttttgataatgtgggcttgtctctgtat---agCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
-------------------gtacttcaaaacacttttaacatatt-------aagatatggaa--aaaagaaaagttgattt--atgagtctcgtatatatat-tgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
| | | |||| | ||| | | || | | || ||||| | | | ||| || | | | | | | | |||||| || || |||| ||||| |||||||||||||||||||| || ||||||||||||||||| ||||| ||||| || ||||||||||| || || |
gtaataattactgtcattagaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0587g00010.t01 (Vitis vinifera), 3'ss of exon 4
---------------------gtacttcaaaa----cacttttaacata-ttaagatatggaa--aaaagaaaagttgattt--atgagtctcgtatatatat-tgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
|| || | || | | || || | | || ||||| | | | ||| || | | | | | | | |||||| || || |||| ||||| |||||||||||||||||||| || ||||||||||||||||| ||||| ||||| || ||||||||||| || | |
gtaataattactgtcattaaaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGGTG
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv17s0000g07440.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------gtacttcaaaacacttttaacatattaagatatggaaaaaagaaaagttgatttatgagtct-cgtatatatat---tgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
|| | | | ||| | | ||| | || ||| | || | || ||| | | | | | | |||||| || || |||| || || |||||||||||||||||||| || ||||||||||||||||| ||||| ||||| || ||||||||||| || || |
gtaataattactgtcattaaaataacttaacatgaccaaactggtcttagccaaagttttgagttaaaaccatattcagttttgataatgtgggcttgtctctgtacagCCTTCCTTTTTTAGCATCAGGGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------gtact-tcaaaacacttttaac----atattaagatatggaaaaaagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
| ||||| | ||| | | ||||| || | || ||||| | || || | | || |||||| ||| || |||| ||||| |||||||||||||||||||| || |||||||||||||||| ||||| ||||| || ||||||||||| || || |
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaaccattttaagttttgataatgtgggcttgtctctgta---cagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S257_1V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------gtacttcaaaacacttttaacatattaagatatggaaaaaagaaa-agttgatttatgagtctcgtatatatat-tgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
| | || || || | | |||| | | | | | | || | | | | || || || || ||||||| | | ||||| ||||| ||||| ||||||||||||||||||||| | ||||||||| |||||| | || ||||| || || ||
gtgagaattttcagaagggttcttaagaccgagttccagtggaaatttgtgctgctc--gactaactcagatgttcaccagatattcaagtgttattcaaatttctgatttaaatgtgcagCCGATGTACTTCAATGTGAGAGCGTACATCAGCTTCATCAAGCCAGACCAAGCTATGTGGTACTTAGCTTGCCAAACTTGTAATCGCAAGGTGGTGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaagatatggaaaaaagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
agttgat putative branch site (score: 5)
aaaaaagaaaagttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttcaaaacacttttaacatattaagatatggaaaaaagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG