Sequence
atgc intronic sequence ATGC exonic sequence...ttttttttcttttcgtgttccttagacatgcttcttactatcttctgtacttgatttgcttgagttaatattgtattcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18620.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 7
-----------------------ttttttt----tcttttcgtgttcct--tagacatgcttcttactatcttctgtacttgatttgcttgagt--taatattgtattcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
||||||| | | | || || || ||| | || ||| || || ||||||| | | ||| | || || || | | ||||||||||||||||| | ||| | || ||||| || | | ||||| | ||||| || || ||||| ||||| || ||||||||||||||||||||||
gtaggtctcccctggctgtgctctttttttggactgtagccatggtcaaagtaattatgttggtttacatcctcaagcatttttttgcttttattctgataattcgttgatgctatgattgatgtttgcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 7
-----------------------ttttttt----tcttttcgtgttcc--ttagacatgctt-cttactatcttctgtacttgatttgcttgagt--taatattgtattcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
||||||| | | | || || || ||| | |||| || || || ||||||| | | ||| | || || || | | ||||||||||||||||| | ||| | || ||||| || | | ||||| | ||||| || || ||||| ||||| || ||||||||||||||||||||||
gtaggtctcccctggctgtgctctttttttggactgtagccatggtcaaagtaattatgttggtttacattcctcaagcatttttttgcttttattctgataattcgttgatgctatgattgatgtttgcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 7
---------------------ttttttttcttttcgtgttccttagaca-tgctt---------cttactatc--ttctgtacttgatttgctt--gagttaatattgtattcatttcatatgtttctac--tacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
|| || | | ||| || ||| || || | | || | | ||| ||| | || | ||||| | | | | | || | |||| ||||||||||||||||| | ||||| || |||||||| | |||||||| | ||||| || || ||||| ||||| || ||||||||||||||||| ||||
gtaggcttctgccagtattgtttgttatatagtgtgtgcacccagaacaatgattgagtaccgattcagtaaccgtgttgtgtcatattagtttttggtttaatctgattctagtccggtttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 7
ttttttttcttttcgtgttccttagacatgcttcttactatcttctgtacttgatttgcttgagttaatattg-tattcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
| | ||| | | | || | | | ||| | | || | | || | || | | || || | | ||| | | | | |||||||||||| |||||| | ||| | |||||||| |||||||| || || |||||||||| || ||||||||||| || ||||||||||| ||||||||||
tatgcttttctagcttattttgaaatctgaactattatttttttgtttgtatgcatc-ctcaaatatttactggtgtgtattatctctttcaatggcacagAATAATCTTCATGAACTCTGGTCTCTTCTCAACTTTCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 7
ttttttttcttttcgtgttccttagacatgcttcttactatcttctgtacttg-atttgcttgagttaatatt-gtattcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
| ||| | | |||| | | | || || | | | ||| | | || | | || | || | ||| | || | ||||||||| || |||||| | ||| | |||||||| |||||||| || || |||||||||| || ||||||||||| || ||||||||||| ||||||||||
--tgcttttctaccttgttttgaaatcttaattattttttttgtttgtttgtatgcatcctcaaatatttactagtgtctattatcacttttattggcacagAATAACCTTCATGAACTCTGGTCTCTTCTCAACTTTCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
-ttttttttcttttcgtgttccttagacatgcttcttac-tatcttctgtacttgatttgcttgagttaatattgt-attcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
| | | || | | | || | || | | || || | | || || ||| ||| | || ||| ||| |||| | || | ||||| ||||| |||||| | ||||| |||||||| |||||| | ||||| | |||||||| || ||||||||||| || ||||||||||| ||||||||||
ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttcttttgac---gttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 7
-ttttttttcttttcgtgttccttagacatgcttcttac-tatcttctgtacttgatttgcttgagttaatattgt-attcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
| | | | | | |||| | | | | | || | || || ||| ||| | || ||| ||| |||| | || | | | ||||| ||||| || ||| | ||||| |||||||| |||||| | ||||| | |||||||| || ||||||||||| || ||||||||||| ||||||||||
tgaaatctgaatcttatttccctttcattggttgcatgtgtaagcgataatgttaatacacttaagtaattaatgtgatttgtttcttttgat---attgcagAACAATCTTCACGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 7
-ttttttttcttttcgtgttccttagacatgcttcttactatcttctgtacttgatttgcttgagttaatattgtattcatttcatatgtttctac-tacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
| ||| | | | | | | | || | || | | | || | || || | || | | || | || ||| | ||||| ||||| |||||| | ||| | |||||||| ||||| || || ||| | |||| |||||| || |||||||| || ||||| ||||||||||| || |
actctttatatatacacatactcttatttgcctatccaataaaaataaaaatgaaaatggtgtagc--atgtgacatccttgctatcttttgctatgtgcagAACAATCTTCATGAACTATGGTCTCTTCTCAACTTTCTACTGCCCGAGATATTTAATTCAGCTGAGACTTTTGATGAATGGTTCCAAATTTCTGGAGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacttgatttgcttgagttaatattgtattcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
agttaat putative branch site (score: 4)
tttctact putative PPT
ttaatattgtattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttttttcttttcgtgttccttagacatgcttcttactatcttctgtacttgatttgcttgagttaatattgtattcatttcatatgtttctactacagAATAATCTCCATGAATTGTGGGCCCTTCTCAATTTTCTTCTCCCTGAGGTTTTTAGTTCAGCAGAAACTTTTGACGAGTGGTTTCAAATTTCTGGTGAAA
- - - - - - - - - - - - - -atgcttc