Sequence
atgc intronic sequence ATGC exonic sequence...atgttactaaatgtcatagacaaaacaattccgcttaagaaaactttaaatcagtttgtttaacatgtgagttcatatttggtttgtacatgatgtatagGTTGCATGAGCGTCTCCAAGAGTGCAACGGGGATGAGATTCTAAAAGCAGAGGCTGGTGCCAAAGTTCAGAAGTTCACTGAATGGGCTCTCAAATGTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59910.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G00260.1 (Glycine max), 3'ss of exon 1
----atgttactaaatgtcatagacaaaacaattccgcttaagaaaactttaaatcagtttgtttaacatgtgagttcatatttggtttgtacatgatgtatagGTTGCATGAGCGTCTCCAAGAGTGCAACGGGGATGAGATTCTAAAAGCAGAGGCTGGTGCCAAAGTTCAGAAGTTCACTGAATGGGCTCTCAAATGTATA
||||| | | | || | | | || ||| ||| | | || || ||| || || | | | | || ||||||||||||||||||||| || ||||| || ||||| | | || ||||| |||||||| || ||||| ||||| |||||||||||||| |||||||||
aattatgttgaaactggaaacaggttatttactgtttttttgctaaaatttctgcagctatagtttttgc---agctcaaatatgaactctgctttttgc-tagGTTGCATGAGCGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA
upper sequence: AT3G59910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G40370.1 (Glycine max), 3'ss of exon 2
----atgttactaaatgtcatagacaaaacaattccgcttaagaaaactttaaatcagtttgtttaacatgtg-agttcatatttggtttgtacatgatgtatagGTTGCATGAGCGTCTCCAAGAGTGCAACGGGGATGAGATTCTAAAAGCAGAGGCTGGTGCCAAAGTTCAGAAGTTCACTGAATGGGCTCTCAAATGTATA
||||| | | | ||| | | | | || ||| ||| | | | || || || || ||| || || | | | | || |||||||||||| |||||||| || ||||| || ||||| | | || ||||| |||||||| || ||||| ||||| |||||||||||||| |||||||||
aattatgttgaaactggaaacagattatgtactgcttttttgctaaaattt----ctgcagctatagtatttgcagctcaaatatgaactctgctttttgc-tagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA
upper sequence: AT3G59910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0094g01540.t01 (Vitis vinifera), 3'ss of exon 4
atgttactaaatgtcatagacaaaacaattccgcttaagaaaactttaaatcagtt---tgtttaacatgtgagttcatatttggtttgtacatgatgtatagGTTGCATGAGCGTCTCCAAGAGTGCAACGGGGATGAGATTCTAAAAGCAGAGGCTGGTGCCAAAGTTCAGAAGTTCACTGAATGGGCTCTCAAATGTATA
| || | || || || | | ||| | | | | | ||| || | |||||| | | | | | || | ||||||||||||||||| || || ||||| |||||||| | | || ||||| || |||||||| || || ||||| |||||||||||||| || |||||
--gagac-aggagttattgataccatgtagttgctgactgttattagatgtttgttgcatgctatccatgtgccaatttgtctcaccattgcttgcttatcagGTTGCATGAGCGTCTTCAGGAATGCAATGGGGATGAAGTCTTGAAGGCAGAAGCAGGTGCCAAGGTCCAAAAGTTTACTGAATGGGCTCTAAAGTGTATT
upper sequence: AT3G59910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S137_124V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------atgttactaaatgtcatagacaaaa-caattccgcttaagaaaacttta-aatcagtttgtttaacatgtgagttcatatttggtttgtacatgatgtatagGTTGCATGAGCGTCTCCAAGAGTGCAACGGGGATGAGATTCTAAAAGCAGAGGCTGGTGCCAAAGTTCAGAAGTTCACTGAATGGGCTCTCAAATGTATA
|||| || ||| || | | || || || | | || ||| || | | || | ||| |||| | | || ||||| | || | || || || |||||||| || || ||| | || || || |||| ||||||||||||| ||||||||||||||||| || |||||
gtagacttttcatatccattcgttcttatcaatttatctcaacttttcccgtcaaaaaaaattcagtacatgtagtcaatcaacattcacttcatctgttgtaattggagaagtatcatgatttatttacgaaatagtcaaatttaacttta--ttgttggt--tttacagGTTACGGGAAAGACTACAGGAATGCAACGGCGACGAAATTTTGAAGGCTGAAGCTGCGGCCAAAGTTCAGAGATTCACTGAATGGGCTCTGAAGTGTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaatcagtttgtttaacatgtgagttcatatttggtttgtacatgatgtatagGTTGCATGAGCGTCTCCAAGAGTGCAACGGGGATGAGATTCTAAAAGCAGAGGCTGGTGCCAAAGTTCAGAAGTTCACTGAATGGGCTCTCAAATGTATA
gtttaac putative branch site (score: 3)
tttgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgttactaaatgtcatagacaaaacaattccgcttaagaaaactttaaatcagtttgtttaacatgtgagttcatatttggtttgtacatgatgtatagGTTGCATGAGCGTCTCCAAGAGTGCAACGGGGATGAGATTCTAAAAGCAGAGGCTGGTGCCAAAGTTCAGAAGTTCACTGAATGGGCTCTCAAATGTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - tactaaa
- - - - - - - - - - -aaaacaa
- - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - taaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttgt