Sequence
atgc intronic sequence ATGC exonic sequence...cataaaaattgcattcgagaattcgttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagTTTGTATGTATGTGTGTTTTGCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30220.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30220.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
cataaaaattgcattcgagaattcgttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagTTTGTATGTATG---TGTGTTTT---GCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAA------------
|| | |||| || ||| | || | ||| || |||| || || | ||| || | || ||| ||| ||| | || ||||||| |||| |||||||| ||||| |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| |
---------------------------acaatgtacacattgaatttgcttgtaacag--atggaatttcgttctttttatacatctttcctgttctgctctta-atggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
upper sequence: AT4G30220.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g08090.1 (Oryza sativa), 3'ss of exon 1
cataaaaattgcattcgagaattcgttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagTTTGTATGTATGTGTGTTT-TGCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAA------------
|| | | | | || || || | | ||| ||| ||| | | ||| | || | | | | || | ||| | | |||||||| | || ||||||||||| || |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| |
----------------------tcat-gatgattattcatggtattcagttccaa--gtggtgcctccatatacatcttgtctatactcttttatatactattaatggattgtttctaaatgcagACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
upper sequence: AT4G30220.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G21250.1 (Glycine max), 3'ss of exon 1
cataaaaattgcattcgagaattcgttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagTTTGTATGTATGTGTGTTTTGCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAA------------
| | || || |||| || || || || || | | | || ||| ||||| | | | | || | ||| |||||||||||||||| |||||||| || || ||||||||||| ||||| || ||| | || || || || || || |||||||
---------------agctgagcgatttcaatgctcacattgagtgta-----gaaggtcacacaatgtgattaattgtgcct-tattttttaatttattctggtcttcctgt---ttttgcagACTATTCCAGTTAACCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCCGTAATTGTGAAACTCAAGTGGGGAATGGAGTACAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagTTTGTATGTATGTGTGTTTTGCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAA
atttgat putative branch site (score: 5)
attagtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataaaaattgcattcgagaattcgttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagTTTGTATGTATGTGTGTTTTGCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
-ataaaaa
- - - - - - - - - - - - - - gaaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttttg