Sequence
atgc intronic sequence ATGC exonic sequenceAGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatctgtttggaaaagttttgattgttgaaattagggtttgaatgtgattttgattctttcatttggggtttaattcgt...
Basic information
species | Arabidopsis thaliana |
transcript | AT1G57660.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G149257_T01 (Zea mays), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatctgtttggaaaagttttgattgttgaaattagggtttgaatgtgattttgattctttcatttggggtttaattcgt--
|| | |||||||| ||||| || ||||||||||| || || || |||||| ||||||| ||||| ||||| ||| | || ||||| ||||||| ||||| | | | | | | | | | || || || | || | | || | || ||| | | |
CGCCGTGCACAAGGGCATGCCGCACAAGTTCTACCACGGCCGCACCGGTCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTTGAGATCAACAAGCAGgtat--aacgcccgcaccagcataccctgtgttgtcattcgttccgtatgcgccgccggtttgctagatgtgtgctgctgctggttgatggcaatacagcga
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G026216_T01 (Zea mays), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatctgtttggaaaagttttgattgttgaaattagg-gtttgaatgtgatttt----gattctttcatttggggtttaattcgt
|| |||||||||| ||||| || ||||||||||| || || || |||||| ||||||| ||||| ||||| ||| | || || || | ||||| ||||| | | || | ||| || || | | | | | ||| || ||| ||||| | || | | ||| | ||| | |
CGCCGTCCACAAGGGGATGCCGCACAAGTTCTACCACGGCCGCACCGGTCGCGTCTGGAACGTCACCAAGCGCGCCATCGGCGTCGAGATAAACAAGCAGgtat--accacacggatcccttttc-gctagctcgctgataggttgctgggcgcaggcagttgaaatcgtttgtgcacggcgcttacgtttagtgcgcggacg--
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA03G36560.1 (Glycine max), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatct----gtttggaaaagttttgattgttgaaattagggtttgaatgtgattttgattctttcatt-tggggtttaattcgt
|| |||||||||| ||||| || |||||||||||||| || || |||||| ||||||||||||| || ||||| ||||| || ||||||||||| ||||| | | |||| || ||| | | | |||| | || | || |||| |||| || | | | | | | ||||
CGCCGTCCACAAGGGAATGCCACACAAGTTCTACCATGGCCGCACCGGTCGCGTCTGGAATGTCACCAAACGTGCTGTTGGGGTCGAAGTCAACAAGCAGgtctcg--cactctcttccttaaccctaacactctatttacttttctgcttctcgatctgttttgttatgtcttttttatcgtgatactatcgcttccaatt---
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA19G39240.1 (Glycine max), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatctgtttggaaaagttttgattgttgaaattagggtttgaatgtgattttgattctttcatttggggtttaattcgt---
|| | |||||||| ||||| || || ||||||||||| || || || ||| ||||||||||||| || ||||| ||||| || ||||||||||| ||||| | || || | || | | || | || || | | |||| ||| || || | || || |
TGCCGTTCACAAGGGAATGCCCCACAAATTCTACCATGGCCGCACCGGACGCGTCTGGAATGTCACCAAACGTGCTGTTGGCGTCGAAGTCAACAAGCAGgtctcacactctt---ccttaaccctagcaccacccttctttccttttctgcttttcgatctgttgtgttttctgtttcttattgtgatattctcgtgtcgaa
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv01s0150g00520.t01 (Vitis vinifera), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgat----tactcaaatctctaatctgtttggaaaagt--tttgattgttgaaattagggtttgaatgtgattttgattctttcatttggggtttaattcgt
|| || |||||||| ||||| || |||||||| ||||| || || || ||||||| ||||| ||||||||| | || ||||||||||||||||||| | | | ||| | ||| | | | || ||| | |||| | | | | || | |||||| | | |||||
CGCCATTCACAAGGGCATGCCCCACAAGTTCTATCATGGCCGCACCGGCAAGGTCTGGAACGTCACCAAGCGTGCCATAGGCGTTGAAGTCAACAAACAGgcatctctcttcttctccttgtctttctctactctgctgcatcattctattatcattattatgaatccag-atctcttcaacattttcatatt---tccaattc--
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S1_780V6.1 (Physcomitrella patens), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatctgtttggaa---aagtt--ttgattgttgaaattagggtttg--aatgtgattttgattctttcatttggggtttaattcgt
||| ||||||||||||||||||| ||||||||||| || || || || | ||||||| ||||| ||||||||||| ||||| | | ||||| ||||| | |||| | || || | | ||| || | || | | | || | | | | | | |||| || | |
AGCCGTCCACAAGGGTATGCCTCACAAGTTCTACCACGGGCGCACCGGCATCGTCTGGAACGTCACCAAGCGTGCCGTCGGTGTCGTGATGAACAAGCAGgtat-gattgaccttctccctccctcccccgaagccgaagccgcctggtcgtgggagctcccccttcctgcttcgttctagggtttttccttctttggctg------
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S107_181V6.1 (Physcomitrella patens), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatctgtt-tggaaaagttttgattgttgaaattagggtttgaatgtgattttgattctttcatttggggtttaattcgt-
||| ||||||||||||||||||| ||||||||||| || || || || | ||||||| ||||| ||||| ||||||||||| | | ||||| ||||| | | | | | |||| || | | | | | ||||| | | || || | | | | | | | | ||||
TGCTGTCCACAAGGGTATGCCTCACAAGTTCTACCACGGACGCACCGGCATCGTCTGGAACGTCACCAAGCGCGCCGTTGGTGTCGTGATGAACAAGCAGgtatggtctctttgtacctct--tcggctgtcgtctacttttggagatgtctgtctggcttaatgactttcgtctgtgggtgcgtcttcgccactattctcg
upper sequence: AT1G57660.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S298_23V6.1 (Physcomitrella patens), 5'ss of exon 1
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatctgtttggaaaagttttgattgttgaaattagggtttgaatgtgattttgattctttcatttggggtttaattcgt------
||| |||||||||| ||||| || ||||||||||| || || || ||| | ||||||||||||| ||||| || |||||||| | | ||||| ||||||| | | | | | ||| | || || || || ||| || | ||| || ||| | | || || |
AGCCGTCCACAAGGGAATGCCCCACAAGTTCTACCACGGGCGCACCGGTATCGTCTGGAATGTCACCAAGCGCGCAGTTGGTGTCGTGATGAACAAGCAGgtgtagtgttttt---tttacgatccaacggcaattcttgtggtttttg---ttgtgccccttgtgtccttacatcagacgcatgtagcattctgtttctgtccatMapped 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|116437489|gb|EG480081.1|EG480081EST: GCATCTAGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAG ATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGG
genomic: GCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgatta ... ggttttatagATTGGGAACAGAATCATAAGGAAGAGGATACATGTGCGTGTGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCTATCCACAAGGGTATGCCTCATAAGTTCTACCATGGTCGTACTGGTCGCATCTGGAATGTCACTAAGCGTGCCGTTGGTGTTGAAGTCAACAAACAGgtgttgattactcaaatctctaatctgtttggaaaagttttgattgttgaaattagggtttgaatgtgattttgattctttcatttggggtttaattcgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaagt