Sequence
atgc intronic sequence ATGC exonic sequencegtaattatttgccttctttctctattgattgtggtcctatcgatttttgtagttaaaacattgaaatgtgtattgcagCTTTTTGATGGACACAATGGTTCTGCAGCAGCTATCTACACTAAAGAGAACCTTTTGAATAATGTATTAGCTGCAATACCTTCTGATCTTAACAGAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G47380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 1
----------gtaattatttgccttctttctctattgattgtggtcctatcg--atttttgtagttaaaacattgaaat------gtgta------ttgcagCTTTTTGATGGACACAATGGTTCTGCAGCAGCTATCTACACTAAAGAGAACCTTTTGAATAATGTATTAGCTGCAATACCTTCTGATCTTAACAGAGATG
| | |||| || || ||| || || ||| | || |||||| | || |||| || |||| || ||||| || |||||||||||||| ||||| || ||||| || | || ||||| ||| | |||||||| ||| |||||| ||||||||||||||||||||||
ataacaaaataaagtagtttgtttttcttttct--tggttttggctttttctgtatttttttccttgttgcatttgcattctctgatgtagaagttttacagCTATTCGATGGACACAATGGATCTGCTGCCGCTATTTATGCCAAGGAGAATCTTCTAAATAATGTTTTAAGTGCAATTCCTTCTGATCTTAACAGAGATG
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G04040.1 (Glycine max), 3'ss of exon 1
------------gtaattatttgccttctttctctattga------ttgtggtcctatcgatttttgtagttaaaacattgaaatgt----gtattgcagCTTTTTGATGGACACAATGGTTCTGCAGCAGCTATCTACACTAAAGAGAACCTTTTGAATAATGTATTAGCTGCAATACCTTCTGATCTTAACAGAGATG
| | | || || | | | | | |||| | | | || | || | | |||| || || ||||| || |||||||||||||| ||||| || ||||| || | || ||||| ||| | || ||||| ||| |||||| ||||||||||||||||||||||
gcagtttatgcaatgaatgcttatgttataacaaaaataaactattttgtatttttttttccttgttgcattggcattctctgatgtagaagttttacagCTATTCGATGGACACAATGGATCTGCTGCCGCTATTTATGCCAAGGAGAATCTTCTAAACAATGTTTTAAGTGCAATTCCTTCTGATCTTAACAGAGATG
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 1
---------------------gtaattatttgccttctttctctattgattgtggtcctatcgatttttgtagttaaaacat-tgaaatgtg--tattgcagCTTTTTGATGGACACAATGGTTCTGCAGCAGCTATCTACACTAAAGAGAACCTTTTGAATAATGTATTAGCTGCAATACCTTCTGATCTTAACAGAGATG
||| ||| | ||| ||| || || | | || ||| | ||| | | ||| || | || ||||| ||||||||||||||||| ||||| || ||||| || |||| ||||| ||| | |||||||| ||| || || ||| | ||||||||||||||||
gttcttaagcactgaatgcttataacacaatgcactatttttcttttcctttt--tttgggcgttttcccttgtttcattttctgatatagagtttttacagCTATTTGATGGACACAATGGATCTGCTGCTGCTATTTATTCTAAGGAGAATCTTCTAAATAATGTTTTAAGCGCGATTCCTCCAGATCTTAACAGAGATG
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 2
-------------------gtaat-tatttgccttctttctctattgattgtggtcctatcgatttttgtagttaa--aacattgaaatgtgtattgcagCTTTTTGATGGACACAATGGTTCTGCAGCAGCTATCTACACTAAAGAGAACCTTTTGAATAATGTATTAGCTGCAATACCTTCTGATCTTAACAGAGATG
||| ||||| |||||| || || | | || | | | | || | | || | ||| | | || ||||| ||||||||||||||||| ||||| || ||||| || |||| ||||| ||| | |||||||| ||| || || ||| | ||||||||||||||||
tgcattgaatgcttataactcaatgtattttttttctttaactttttttggggggcattttcacttgtttcattttctgattctgatagcgtttttacagCTATTTGATGGACACAATGGATCTGCTGCTGCTATTTATGCTAAGGAGAATCTTCTAAATAATGTTTTAAGTGTGATTCCTCCCGATCTTAACAGAGATG
upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 2
-----------------gtaattatttgc-cttctttctctat-tgattgtggtcctatcgatttttg-tagttaaaac--attgaaatgtgtattgcagCTTTTTGATGGACACAATGGTTCTGCAGCAGCTATCTACACTAAAGAGAACCTTTTGAATAATGTATTAGCTGCAATACCTTCTGATCTTAACAGAGATG
||||| | | | | ||||| |||| | | | ||||||| ||| | | | | | || | | |||||||| ||||||||||| ||||| |||||||| ||||| ||| | |||||||| ||| | || ||||| |||||||| || ||| | || |||| ||||||||
atctattgttgcttatatctcatatttacacaacagtttctatatgataatatatatgtgtatttttggtaggtggatcttactaaacctttttttgcagCTATTTGATGGACATAATGGATCTGCAGCTGCTATATACTCAAAAGAGAATCTTCTAAACAATGTTTTAGCTGCTATTCCTCCAGAACTTAGCAGAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgattgtggtcctatcgatttttgtagttaaaacattgaaatgtgtattgcagCTTTTTGATGGACACAATGGTTCTGCAGCAGCTATCTACACTAAAGAGAACCTTTTGAATAATGTATTAGCTGCAATACCTTCTGATCTTAACAGAGATG
tattgat putative branch site (score: 3)
atttttgtagttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattatttgccttctttctctattgattgtggtcctatcgatttttgtagttaaaacattgaaatgtgtattgcagCTTTTTGATGGACACAATGGTTCTGCAGCAGCTATCTACACTAAAGAGAACCTTTTGAATAATGTATTAGCTGCAATACCTTCTGATCTTAACAGAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG