Sequence
atgc intronic sequence ATGC exonic sequencegcatgtatcctatttagcatttcttttaactctgccatttttctccaacacttggtctataacttagtctaattttgcagCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61140.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g02540.1 (Oryza sativa), 3'ss of exon 3
gcatgtatcctatttagcatttcttttaactctgccatttttctccaacacttggtctataacttagtctaat--------tttgcagCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG
| || | || || || | | | | || | || | ||| ||| || | | | ||| ||| ||| ||||| || ||||| | || ||||| || || ||||||| |||||||| |||||||||||| | || ||||||||||||||
gtttgctttctgttc-gcttatttcctgtctgggtgtgttcctttaaaccattgtactcagatatgattgaataaacattttttacagAGCAAAGTTATCGACAACAGTAATTTCCGAAACTTTCTGGAGCTGGTGCCTGAAGTGAGGGAACTTGTTAATGATTTCTATTCAAG
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G062210_T01 (Zea mays), 3'ss of exon 3
----gcatgtatcctatttagcatttcttttaactctg--ccatttttctcca--acacttggtctataacttagt-ctaattttgca--gCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG
|| | || ||| | | | | | || ||||||| ||| || | | | | | | | |||||||| | |||||||||||||||||||||||||| || || ||||||| |||||||| || ||||| || | || ||||| ||| ||||
gtttgccatttcagtacttatttgtcttgtggaatgtgttccattttatgccactgttctcgaaatgtgattgcttgcgcattttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 3
gcatgtatcc--tatttagcatttcttttaactctgccatttttc--tccaacacttggtctataacttagt---ctaattttgcagCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG
|||| ||| | ||| | ||| || | | | | | | ||| | | ||| | | | | | || |||| | ||||| || |||||| ||||||||||||| ||||| ||| |||| ||||| || ||||| ||||| | ||||||||||||||
gcatctattgagtgtttttccttttcaatagttgtttttctctatggtttcatgattgctttctaattgaatgctttcacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCTGAAGTAAGGGAGCTTATTCATGATTTCTATTCAAG
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------gcatgtatcctatt----tagcatttcttttaactctgccatttttctccaacac---ttggtc---tataacttagtctaattttgcagCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG
|| | || | |||| ||| | | | | | | | | || | || || | || | | || | || ||||| |||||||| ||||||||||| ||||| |||||||| || ||||| ||| | || || ||| | || || ||| | ||
gtaaaataccaaaccctcttttaattattttttttagtgatctttctggcttataaactctgctatcgtagcttttatcatgagttagtaagatggatttaattcattttaatcatgtccaatctgtcgccaattggtagAGTAAAGTGATTGACAACATCAACTTCCGCAATTTTTTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaactctgccatttttctccaacacttggtctataacttagtctaattttgcagCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG
tataactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgtatcctatttagcatttcttttaactctgccatttttctccaacacttggtctataacttagtctaattttgcagCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT