Sequence
atgc intronic sequence ATGC exonic sequencegtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62790.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------------------------------gtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataa-catgtattt-gttttgttccac-agGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT
| | || | ||| ||| | || ||| || || || || | | || || || ||| |||| | | |||||||||||||| | |||||| |||| ||||| |||||||| |||| || | ||||||||||| ||||| || ||| | ||| || || || || |
gtgagtcctacagcacagctatggaaaatgtttagcggttatgctcaactgcagtggattttaaactgttaatgcatgcacacttaatcctgatatggc-aaccgtattttcatgtttacgtttggcttaatattttttttcaagtattcatgaagttctgtttctccagGATTCATCTGTGTTGGCTCAACTGGGATGGCCAGATATGCGGATACCAATCTTATACACCATGTCTTGGCCAGACAGAATCTATTGCTCAGAGGTCACCT
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 9
-------------gtcttgctg-aaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT
|| || | | || | | || | || ||| | | | || | | ||||| | | || | | || | |||||||||||||| || ||||||||||| ||||| |||||||| |||| || | |||||| | || ||||| |||||| | ||| || || || || |
attatttcaggtcgttatggtacatgcagaattgtttatgtaatggctttacatatggtttaatattgtctgtagcattcatgttcttctattttcccagGATTCATCTGTCCTAGCTCAATTGGGATGGCCGGATATGCGGATACCAATCTTATACACCTTATCGTGGCCAGATAGAATCTATTGCTCGGAGGTCACGT
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 9
--------------gtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccac-agGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT
| | | | | |||| | | | | ||| ||| | | | | | || | | | || || ||||| || ||||||||||||| || ||||| ||||| ||||| |||||||| ||||| || | |||||| | |||||||| |||||| | ||| ||||| || || |
ttgttttagatcatttatggttcatacataattgtttctgtaattgatttatatatggtttagtattgtctttggtattcatgttc-ttctgttctactagGATTCATCTGTCCTAGCTCAGTTGGGATGGCCAGATATGCGGTTACCAATCTTATACACCTTATCATGGCCAGATAGAATCTATTGCTCTGAGGTCACCT
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 9
---------gtcttgctgaaacattactaactaaatta-----ttattttt--ccggttttaaaaaaataactgtataacatgtatttgttttgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT
| | |||| || || ||| | ||| || | | |||| | || | ||| | | || || ||||| |||||||||||| ||||| |||||||| ||||||||||||||||| || || ||||| || | |||||||| || || || |||||||||||| ||||
aacttgtgtataatatagaaagggtatcaaagaaaggagaaaaatatcattaaacattgttaatcatattatctaatactaaatcatttcttgattcca--gGATTCATCTGTTCTTGCACAATTGGGGTGGCCTGATATGCGTTTGCCAATCCTCTATACATTATCATGGCCTGACAGGATTTATTGTTCTGAAGTCACTT
upper sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 9
---------gtcttgctgaaa----cattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgtt-ccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT
| | |||| || | || | | | | ||| | | | ||| | | || ||| | |||||||||||||| ||||| || ||||| ||||||||||||||||| || || ||||| || | |||||||| || || || ||||||||||| ||||
aacttgtgtataataaagaaaagggtatagaagaaagaagaaaaagatcattaaccattgtttaatcattatctaatactaaattatttcttgattccagGATTCATCTGTTCTTGCACAGTTGGGGTGGCCTGATATGCGTTTGCCAATCCTCTATACATTATCATGGCCTGACAGGATTTATTGTTCTGAAGACACTTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164163268|gb|ES024308.1|ES024308EST: ATCATACATTCCATGATTGAAACACAG GATTCATCTGTGCTTGCTCAATTGGGTTGGCC
genomic: ATCATACATTCCATGATTGAAACACAGgtcttgctga ... tgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCC
EST:
gi|164020276|gb|ES076441.1|ES076441EST: GTCATTCATCCTCAAAGTATCATACATTCCATGATTGAAACACAG GATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTAC
genomic: GTCATTCATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctga ... tgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTAC
EST:
gi|125003558|gb|EL075827.1|EL075827EST: CATCCGCAAAGTATCATACATTCCATGATTGAAACACAG GATTCATCTGTNCTTGCT
genomic: CATCCGCAAAGTATCATACATTCCATGATTGAAACACAGgtcttgctga ... tgttccacagGATTCATCTGTGCTTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT
ttttgttcc CT-rich tract
ttttaaaaaaataact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttgctgaaacattactaactaaattattatttttccggttttaaaaaaataactgtataacatgtatttgttttgttccacagGATTCATCTGTGCTTGCTCAATTGGGTTGGCCTGATATGCGTTTACCGATTCTCTACACCATGTCATGGCCCGATAGAGTTCCTTGTTCTGAAGTAACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG