Sequence
atgc intronic sequence ATGC exonic sequencegttagtctactgttaggctttagtgatatcacttcttttggtttcttagctttctgtttccttccagttgtgagtaaatgaggccttcttctcctggttgaaaaaaaaaactctgtagAAGAAGTTTTCGGAGAAGTGAAACCGATTCTTAGATCTGCTCTTGATGGTCACAATGTATGTGTCTTGGCGTATGGTCAAACGGGAACTGGCAAGACTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27950.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g42800.1 (Oryza sativa), 3'ss of exon 1
----gttagtct-actgttaggctttagtgatatcacttcttttggtttcttagctttctgtttccttccagttgtgagtaaatgaggccttcttctcctggttgaaaaaaaaaactctgtagAAGAAGTTTTCGGAGAAGTGAAACCGATTCTTAGATCTGCTCTTGATGGTCACAATGTATGTGTCTTGGCGTATGGTCAAACGGGAACTGGCAAGACTTT
||| ||| ||| | | | || | || | || | || |||| | ||| || |||| | | | || || || ||| | || | ||| || |||||| ||||||||| || ||||| |||||||| |||||||| |||||||| ||| | | || ||||||||||| || || || ||||| |
gtatcttactcttactcacgagatctcgtcactgaacactgctattcttttcagttttcactgctctt---attctgagagtgtaactcgtttcacttcttgttcataa---------ttcagAGGATGTTTTCCAAGAAGTGAAGCCAATTCTCAGATCTGCACTTGATGGGCACAATGTCTGTATTCTTGCTTATGGTCAAACTGGGACAGGAAAGACCTA
upper sequence: AT5G27950.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0030g01360.t01 (Vitis vinifera), 3'ss of exon 3
gttagtctactgttaggctttagtgatatcacttcttttggtttcttagctttctgtttccttccagttgtgagtaaatgaggccttcttctcctggttgaaaaaaaaaactctgtagAAGAAGTTTTCGGAGAAGTGAAACCGATTCTTAGATCTGCTCTTGATGGTCACAATGTATGTGTCTTGGCGTATGGTCAAACGGGAACTGGCAAGACTTT
||| | | | | | || | || | |||| | || | ||| |||| ||||| ||||| ||| | | | || || | |||||||||||||||| ||||| | || || | || |||||||| || || || ||||| |||||||||||| | || || ||||||||||| || ||||||||||| ||
----gtc-agtatcaaatct---ccatctgtttttctcaagtttaattatcttat-tttgtttccggttgt-agtaa--gagactctatcctgctttt-------gaaaactctgtagAAGATGTTTTTGTTGAGGTCGAGCCAATTCTTAGGTCGGCACTGGATGGGCACAATGTATGTATATTAGCTTATGGTCAAACTGGCACTGGCAAGACATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagttgtgagtaaatgaggccttcttctcctggttgaaaaaaaaaactctgtagAAGAAGTTTTCGGAGAAGTGAAACCGATTCTTAGATCTGCTCTTGATGGTCACAATGTATGTGTCTTGGCGTATGGTCAAACGGGAACTGGCAAGACTTT
ttgaaaaaaaaaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtctactgttaggctttagtgatatcacttcttttggtttcttagctttctgtttccttccagttgtgagtaaatgaggccttcttctcctggttgaaaaaaaaaactctgtagAAGAAGTTTTCGGAGAAGTGAAACCGATTCTTAGATCTGCTCTTGATGGTCACAATGTATGTGTCTTGGCGTATGGTCAAACGGGAACTGGCAAGACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA