Sequence
atgc intronic sequence ATGC exonic sequence...tgcttgcttatctatggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G05780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 1
-tgcttgct-tatctatggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
| | | | ||| | | | || | | | | ||| || ||||| | | | | || | | || | | ||| |||||| ||||||||||||||||| || || || |||||||| ||||| ||||| ||||| |||||||||||| |||||||||||| |||||||
cagttagatctattgacgtggaatgcccgtgcggaattgattagatctgtgacgttgtcccgggggtgacttgc-taaatccgct-acttgattttttgcagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCACGAGTCAATGTTCTCCATGTTCAAGAGGATTAATG
upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G368908_T02 (Zea mays), 3'ss of exon 1
--tgcttgcttatctatggacactg-tcactagaaacctctttaatagatggatgttgttt-acatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
| | | | | || ||| ||| | | || || || ||||| | ||| || || || | | || |||||||||| ||||||||||||||||| || || || |||||||| ||||| ||||| |||||||| || |||||| |||||||||||| ||||| |
tctattgacgtggattgccacgctgctcatgcgtgattgattagatctgtgatcgttgtcccgggtgtgacttgctg--aatccgctacttgtttt--ttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG
upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 1
tgcttgcttatctatggacactgtcactagaaacctctttaatagatggatgtt--gtttacatatgaatt-----cgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
|| || || | ||| || | || | | || | |||| ||| |||||| | | | | | | |||| | |||||||||||| || |||||||| || || ||||||||||||||||| ||||| |||||||| || ||||| |||||| || ||||| |||
-----gcataag-attgttacttccaaaatgaatttttgagatgtttcaatgtgcaatttgacagtgaattgtctgtctctcactacttggttatctaatttgacaGTGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCGATGTTTTCCATGTTTAAAAGAATAAAT-
upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 1
tgcttgcttatctatggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaatt---cgtgt-taacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
| || | | | | | | || | ||| | | ||| | |||||| || | | || ||| | | | |||||||||||| || |||||||| || || ||||||||||||||||| ||||| |||||||| || ||||| |||||| || ||||| ||||
---tgaattttgttgaaatgattctatgtgcaatttagaaaattaacacctattggg-gtgtgtgaattgtctgtctctcactacttggttatctaattgacagTGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG
upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 3'ss of exon 1
---tgcttgcttatctatggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
| | ||| | |||| || | || | | | ||| || | |||| || || ||| || || || ||| |||||||||||| || |||||||| |||||||| || || |||||||| ||||||||||| || |||||||| ||||||||||||||| ||||
aaacagattagggtttata-atactggcattgttaagaggggacaaaaaaaattgtcaatt-cttatggcttt-tgctaaatggtagagtgctgtgtttgcagTGCCCTTTGAAGAAGATGACAAGGACCCAAGTATATGTTTTCTTGACCACAACTACCACGAATCAATGTTTTCCATGTTCAAGAGAATAAATG
upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 1
-tgcttgcttatctatggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaatt-gtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
| || || | | | | | | | | ||| | ||| | || ||| || | | ||| || | |||||||||||| || |||||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||| ||||||||||||||| ||||
ccaagcggagggttagggtttatagtattggcattgttaagagggtacaagaattgccaat-tattggctgttgctaa-atagtagggtgttgtgtttgcagTGCCCTTTGAAGAAGATGACAAGGACCCAAGCATATGGTTTCTTGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG
upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 1
tgcttgcttatct---atggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
| | | | | | | | || | | | | | | | | || ||| || | || | | | || | | || |||||||||||||||| |||||||| || | ||||| ||||| | || |||||||| |||||| | |||||| ||||||||||||||||||| |
ggactataaaattggaagaaaaaataataccatagggcgatatga-aattctattttggg-actgaaaaacgatcgcgatggggatgggag-tgattttttagTGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG
upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 1
tgcttgcttatctatggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
||||| | | | || | | | | ||| | || || | | | | ||||| || ||| | ||| ||| || ||||| |||||||||| ||||||||||| |||||| | ||||||||||| || || | ||||| | ||||||||| | || ||||
-----------gtatggccgat-ttgtaggaga--tttcgaggagagaatttctggtttcctggggagtcgtgagaa----ttgttcttccttcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATGMapped 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|152033865|gb|BP818102.2|BP818102EST: TCTGGGGAGCAGCTCTCGTGGTGTTGTTGATGTCACCAACAGCTATGCAG TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACA
genomic: TCTGGGGAGCAGCTCTCGTGGTGTTGTTGATGTCACCAACAGCTATGCAGgtatgcctta ... tgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACA
EST:
gi|47831858|gb|CK121542.1|CK121542EST: TCTGGGGAGCAGCTCTCGTGGTGTTGTTGATGTCACCAACAGCTATGCAG TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACA
genomic: TCTGGGGAGCAGCTCTCGTGGTGTTGTTGATGTCACCAACAGCTATGCAGgtatgcctta ... tgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
tttacatatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcttgcttatctatggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA