Sequence
atgc intronic sequence ATGC exonic sequencegttttgtcccttggctcttgtttcttcgtttctatggtttttagtcatactttgagattcttttcattgttgtatcaaatttagGTACCTGTATCGATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G77090.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 2
gttttgtcccttggctcttgtttc---ttcgtttctatggtttttagtcata--ctttgagattc----ttttcattgttgta----tcaaatttagGTACCTGTATCGATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTA
|| | ||| ||| | ||| | ||| | |||| | |||| ||| | || |||| | | ||| ||||| || || ||||| ||||||||||||||||||||||| ||| || | ||||| | | | || | || ||||||| || ||||||| || |||| |
gtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgttccaatttttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTTGCGAATTCCAAGCAGGGACGTTTGTTCGTCGTTGTAGCACCGGTTCGCA
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 2
---------gttttgtc-ccttggctcttgtttcttcgtttctatggtttttagt---catactttgagattcttt-tcattgttgtatcaaatt--tagGTACCTGTATCGATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTA
||| || ||| | ||||| ||| |||| || | | | ||| || ||| || | | ||| || ||||||| ||||| || || |||||||||||||| ||||| || ||||||||||| || |||| ||||| ||||||| ||| ||||| |||||||||||||
tgtaatcacatttcttcacctagaggacattttctctctttttatgtccttctgcttgcttgcttctgtatacttaatccaggatacatctgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTTGCCAGCTCTAAGGAAGGACGTTTGTTTGTCATTGTTGCTCCTGTTCTTA
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 2
---------gttttgtcccttggctcttgtttcttcgtttctatggtttttagtcatactt--tgagattcttttcatt---gttgtatcaaatt--tagGTACCTGTATCGATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTA
||| || | | | ||| || || | | || || | | ||| | | ||||| | || ||| || ||||||| ||||| || || |||||||||||||| ||||| || ||||||||||| || |||| ||||| ||||||| ||| ||||| |||||||||||||
tgttctcacatttcttcacctagaggacattttctctctttttttgtccttctgcttgcttgcttgtgtatacttcatccaggatgcatctgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTTGCCAGCTCTAAGGAAGGACGTTTGTTTGTCATTGTTGCTCCTGTTCTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatggtttttagtcatactttgagattcttttcattgttgtatcaaatttagGTACCTGTATCGATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTA
ttgtatcaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgtcccttggctcttgtttcttcgtttctatggtttttagtcatactttgagattcttttcattgttgtatcaaatttagGTACCTGTATCGATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG