Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttatagagacagctatttctctaacaacagtgttttactagcactatatagtttttgtcctcttttcaagattttaactgtgaaggctgttactgatatagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G11510.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 5
gtatgcttatagagacagctatttctctaacaacagtgttttactagcactatatagtttttgtcctcttttcaagattttaactgtgaaggctgttactgatatagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
|||||| || | || | | || | | || | || | || || | | | || | | | | ||| | | ||| || |||||||||||| ||||| || |||| ||||||||| || || ||||| |||||||| || | || || | |||||||| ||| ||||| |||| ||||
-tatgctaatttatttcttaatgtgcatgccattatttttaatcgagtatcat-tactgtggattctacgtcttaaagatggactatctaatctgc-----atttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
upper sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 3
gtatgcttatagagacagctatttctctaacaacagtgttttactagcactatatagtttttgtcctcttttcaagattttaactgtgaaggctgtta-ctgatatagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
| || | | | | | | | || || | ||| | |||||| | | || | || | |||| || | ||| ||||| ||||||||||||||||| || || ||||||||||| || || ||||| |||||||| ||| | ||| |||| ||||||| || ||||| |||| ||||
--aggcatcatatggta--tgtctttgcaaattcattcaattatgggtactataaatgtgttaactgtagttt----ctctaaccatggattagcttatctgattcagGTGGCACAATCATCTTAACCCAGCCATAAACAAGGAGGCATGGACGCAAGAAGAGGAGATTACTCTTATTCATGCTCATAGGATGTATGGAAATAAATGG
upper sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G08550.1 (Glycine max), 3'ss of exon 6
gtatgcttatagagacagctatttctctaacaacagtgttttactagcactatatagtttttgtcctcttttcaagattttaactgtgaaggctgttactgat--atagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
|| ||| || | | | | | | | | | ||| | | | | | | | | | || || |||||||||| |||||||| |||||| | ||||| || ||||| ||||| |||||||| ||| || ||| || || || ||||| || ||||| || ||||||
--------attcagattatctttatccctgttgcctcataccatca-tattggagaatttcgatggatgtagttaattctcgtttatataattttgtaaaaatgtatagGTGGCATAATCATCTTAATCCTACTATAAATAAGGAAGCATGGACGCAAGAAGAGGAGTTGGCTCTTATACGCGCACATCAGATTTATGGGAACAGATGG
upper sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 5
-gtatgcttatagagacagctatttctctaacaacagt-gttttactagcactatatagtttttgtcctcttttcaagattttaactgtgaaggctgttactgatatagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
|||| |||| | | | | | | ||| ||| | | | || | ||||| | || || | || || | ||||||||||||||||| ||||||||||||||||| ||||| |||||||||||||| || ||| | | |||| |||||||||||| ||||| || | |||
tctatgattattctatgatgtttcttttggcttttgatcactttgttaggatgagaatgt----gctactttttcta---cttgcatggattgatccttcct--ttcagGTGGCACAATCATCTAAATCCTGCCATAAACAAGGAAGCATGGACTCAAGAAGAGGAACTGGCTTTAATTCATGCTCATCAAATTTATGGGAACAAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagtttttgtcctcttttcaagattttaactgtgaaggctgttactgatatagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
tactgat putative branch site (score: 2)
ttttcaagattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttatagagacagctatttctctaacaacagtgttttactagcactatatagtttttgtcctcttttcaagattttaactgtgaaggctgttactgatatagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT