Sequence
atgc intronic sequence ATGC exonic sequencegtacgcttttggtttgtaattcttatgtacttattcagactaagggtggctgactgtaatttcataatgactgtagGAACTGGTCCAGCAGATGGCAAATGTACAATACACTGAGAACCTTACTGAAGATCAGTTGGATGCCATGGCAGGAAGTGAGACTTTACGTTATCATGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G24706.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G24706.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os01g68810.1 (Oryza sativa), 3'ss of exon 20
gtacgcttttggtt--tgt--aattcttatgtact-tattcagactaagggtggctgac-tgtaatttcataatgactgtagGAACTGGTCCAGCAGATGGCAAATGTACAATACACTGAGAACCTTACTGAAGATCAGTTGGATGCCATGGCAGGAAGTGAGACTTTACGTTATCATGCAA
|| || ||| | ||| | | | || || | | ||| |||| | |||| | || | ||| ||||||| | ||||| ||||||||||| ||||||||||||||| | ||||| || ||| | ||||| |||||||| ||||| || || || ||| ||
gtctactactggctactgtcaagcttccccttgctaccttggaattgtatgtgtctgaagtctaatatgatcactcctgcagGAACTCATTCAGCAAATGGCAAATGTGCAATACACTGAGAACATGACTGAGGAGCAGGTTGATGCTATGGCAGGGAGTGAAACATTGCGGCTTCAAGCTT
upper sequence: AT1G24706.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA08G05320.1 (Glycine max), 3'ss of exon 17
---------------------------------------------------gtacgcttttg--gtttgtaattcttatgtacttattcagactaagggtggctgactgtaatttcataatgactgtagGAACTGGTCCAGCAGATGGCAAATGTACAATACACTGAGAACCTTACTGAAGATCAGTTGGATGCCATGGCAGGAAGTGAGACTTTACGTTATCATGCAA
|| ||| || | | ||| ||| | | | || | || | || ||| | |||| || | || || ||||| ||||| || ||||| |||||| | ||||| || ||||||||||| |||||||| ||||||||| | | ||||| ||||
gtttttcttttttctttttctttgtctgtcttttttattcccaaataaataataatcttatgtgagatatggctctcatgaaaat-tccaaatgttggctataaataaatatttttgctggtttttcagGAGCTTATTCAACAAATGGCTAATGTCCAGTACACGGAGAACTTGACTGAGGAACAGTTGGATGCAATGGCAGGGAGTGAGACTCTCAGATATCAAGCAA
upper sequence: AT1G24706.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA05G34330.1 (Glycine max), 3'ss of exon 20
----------------------------------------------------gtacgcttttggtttgtaattcttatgtacttattcagactaagggtggctg--actgtaatttcataatgactgt-agGAACTGGTCCAGCAGATGGCAAATGTACAATACACTGAGAACCTTACTGAAGATCAGTTGGATGCCATGGCAGGAAGTGAGACTTTACGTTATCATGCAA
| | | || | || || | || | | | | || | ||||| | | | || | || | |||| || | || || ||||| ||||| || ||||| |||||| | ||||| || ||||||||||| ||||| || ||||||||| | | ||||| ||||
gtttttcttttttgtttttctttgtctttgtcttttttcccccacgaataaagaataatctta-tgtgagatatggctctaatgaaaaatccaaatgttggctataaataaatatttttgctggttcccagGAGCTTATTCAACAAATGGCTAATGTCCAGTACACGGAGAACTTGACTGAGGAACAGTTGGATGCAATGGCTGGGAGTGAGACTCTCAGATATCAAGCAA
upper sequence: AT1G24706.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv01s0011g06090.t01 (Vitis vinifera), 3'ss of exon 1
----------gtacgcttttggtttgtaattcttat--gtacttattcagactaagg-------gtggctgactgtaatttcataatgactgtagGAACTGGTCCAGCAGATGGCAAATGTACAATACACTGAGAACCTTACTGAAGATCAGTTGGATGCCATGGCAGGAAGTGAGACTTTACGTTATCATGCAA
| | ||||| || | |||| | || ||| || | | || | || ||| |||| || | |||||||| |||| |||||||||||||| || ||||| |||||||| ||||| || ||||||||||| |||||||| |||||||| | || ||||| || |
gtatttcttgttgtacatttggattattccaattatcagacctcattaagccctaaactttgcagttattttttggaatctcatgattggtacagGAACTGATCCAACAGATGGCAAATGTTCAGTACACGGAGAACCTGACTGAGGAACAGTTGGATGCTATGGCAGGGAGTGAGACCCTCCGGTATCAGGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatgtacttattcagactaagggtggctgactgtaatttcataatgactgtagGAACTGGTCCAGCAGATGGCAAATGTACAATACACTGAGAACCTTACTGAAGATCAGTTGGATGCCATGGCAGGAAGTGAGACTTTACGTTATCATGCAA
ggctgac putative branch site (score: 3)
tgtaatttcataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcttttggtttgtaattcttatgtacttattcagactaagggtggctgactgtaatttcataatgactgtagGAACTGGTCCAGCAGATGGCAAATGTACAATACACTGAGAACCTTACTGAAGATCAGTTGGATGCCATGGCAGGAAGTGAGACTTTACGTTATCATGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA