Sequence
atgc intronic sequence ATGC exonic sequence...tgaatttggtgtatgatagatattaaacccttctgttgctatcataactgtatgatttgtaattttgttgatggttttaagtttatatgttgatgagcagGAGATGTTCATGGTCAGTTTCCAGACCTCTTGCGGTTGTTTGAGTATGGTGGTTATCCACCAGCTGCGAACTACTTGTTTCTTGGGGATTATGTTGATCG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11240.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 1
----tgaatttggtgtatgatagatattaaacccttctgttgctatcataactgtatgatttgtaattttgttgatggttttaagtttatatgttgatgagcagGAGATGTTCATGGTCAGTTTCCAGACCTCTTGCGGTTGTTTGAGTATGGTGGTTATCCACCAGCTGCGAACTACTTGTTTCTTGGGGATTATGTTGATCG
| || | | | | || ||| || || | | | || | ||||| | | | || || | || | | || |||||||| | ||||| |||| | | || || | ||||| ||||||||||| || | ||||||| || |||||||||||||| || ||||||||||| ||
acgctaaaacttct-tgttctaactataaacaatttgtaaca-tgttgtaga-atgtgatt-gcatcatgcttaccatcattctgcctacttactcattgacagGAGATATCCATGGCCAGTATTCTGATCTTCTTCGGTTATTTGAGTATGGGGGCTTCCCACCAGAGGCAAACTACTTGTTTCTAGGTGATTATGTTGACCG
upper sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G041822_T02 (Zea mays), 3'ss of exon 1
tgaatttggtgtatgatagatattaaacccttctgttg-ctatcataactgtatgatttgtaattttgttgatggttttaa--gttta--tatgttgatgagcagGAGATGTTCATGGTCAGTTTCCAGACCTCTTGCGGTTGTTTGAGTATGGTGGTTATCCACCAGCTGCGAACTACTTGTTTCTTGGGGATTATGTTGATCG
| || ||| ||| | || ||| || | | || |||| | || |||| ||| ||| |||| | ||| | ||||| ||||| ||||| |||| | |||||||| | || || |||||||||||||| |||||||||| ||| || || |||| || || || |||||||||||
--atgttagtgcatgctctgta---aacttgtcaactaacaatttgcgatgtacattgatgcatattgtggataacgataaccatttaacttctttgctatgcagGGGATGTCCATGGCCAGTATTCAGACCTCCTTCGATTATTTGAGTATGGTGGCTATCCACCAGATGCAAATTATCTGTTCCTGGGTGACTATGTTGATCG
upper sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 1
--------tgaatttggtgtatgatagatattaaacccttctgttgctatcataactgtatgatttgtaattttgttgatggttttaagtttatatgttgatgagcagGAGATGTTCATGGTCAGTTTCCAGACCTCTTGCGGTTGTTTGAGTATGGTGGTTATCCACCAGCTGCGAACTACTTGTTTCTTGGGGATTATGTTGATCG
||| || ||| ||| | | ||||| | || || | || || || | | || || | || ||| | | | || | ||||| ||||| |||||||||| | ||||||| | || || |||||||||||||| |||||||||| ||| || || |||| || || || ||||||||| |
agtaaccttgatgttagtgcatgct---ttgtaaactcgtcaattaacaaaatggatgcattaatgtggataatgataatcatttaacttctttac-----tatgcagGGGATGTCCATGGTCAGTATTCAGACCTTCTTCGATTATTTGAGTATGGTGGCTATCCACCAGATGCAAATTATCTGTTCCTCGGTGACTATGTTGATAG
upper sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 2
-tgaatttggtgtatgatagat-attaaacccttctgttgctatcataactgtatgatttgtaattttgttgatggttttaagtttatatgttgatgagcagGAGATGTTCATGGTCAGTTTCCAGACCTCTTGCGGTTGTTTGAGTATGGTGGTTATCCACCAGCTGCGAACTACTTGTTTCTTGGGGATTATGTTGATCG
| | ||| | ||| || | ||| | | || | | | | | || | | || | | | ||| ||| | ||||| || | ||||| |||| | | ||||||||| | ||||| |||||||||| |||||| | || |||||||||||| | |||||||||||||| |
tttattttattctattttattttattttaagcacctactagttacgtgctgtttcttttcttgaagctggtcactgacaagtgttggcatgacact--gcagGTGACATCCATGGGCAGTATTCCGACCTCTTGAAACTTTTTGAATATGGTGGTTTTCCACCTGAGGCCAACTACTTGTTTTTAGGGGATTATGTTGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactgtatgatttgtaattttgttgatggttttaagtttatatgttgatgagcagGAGATGTTCATGGTCAGTTTCCAGACCTCTTGCGGTTGTTTGAGTATGGTGGTTATCCACCAGCTGCGAACTACTTGTTTCTTGGGGATTATGTTGATCG
ttttaagtttatatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaatttggtgtatgatagatattaaacccttctgttgctatcataactgtatgatttgtaattttgttgatggttttaagtttatatgttgatgagcagGAGATGTTCATGGTCAGTTTCCAGACCTCTTGCGGTTGTTTGAGTATGGTGGTTATCCACCAGCTGCGAACTACTTGTTTCTTGGGGATTATGTTGATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- aatttgg
- - - - - - - - - - - ttaaacc
- - - - - - - - - - - - - - - - ctgttgc
- - - - - - - - - - - - - - - - - - - - - cataact
- - - - - - - - - - - - - - - - - - - - - - - - - - -gatttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttta