Sequence
atgc intronic sequence ATGC exonic sequenceAAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCACCCATTGCAGTTGgtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16780.1 |
intron # | 14 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 5'ss of exon 13
AAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCACCCATTGCAGTTGgtgagt-cagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataag-------gaaccaacgctctctatttgatgtccacag
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AAGCCTGATTACGGTCGTTGTGTTGCAATTGTGGCATCTGCTTCCTTGAGGGAAATGATAAGGCCGGGGGCTTTAGCCATTATATCACCCATGGCTGTTGgtaagttctatagatatgggggttattgcatttttgttctagcgttgggtacttttttttttttgaaaatggggaaaccaatcatggtttgcag
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 5
AAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCACCCATTGCAGTTGgtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacag
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AAGCCGGATTATGGACGCTGTGTTGCAATTGTGGCATCTGCATCCTTGAGAGAAATGATAAAGCCTGGAGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtct-------tgtaggtcatatctgtg----gtgactggcactcg-atgcttttctaatttggtttacgcggtttgcag--
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G075900_T01 (Zea mays), 5'ss of exon 13
AAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCACCCATTGCAGTTGgtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacag
||||| |||||||| || |||||||| ||||| || ||| || | || || |||||||||||||| || ||| | || || ||||||||||| || ||||||||||| ||| || | | ||| || | | || | | | || ||| || ||| |||
AAGCCCGATTATGGACGCTGTGTCGCAATTGTGGCCTCTGCATCCTTAAGAGAAATGATAAAACCTGGGGCTCTAGCAATTATATCACCCATGGCCGTTGgtgagtct-------tgtaggccatgtttgtgg--tgactagcactca-atgtgcttttctaatttgaattatgtg--gtctgcag
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 13
AAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCACCCATTGCAGTTGgtgagtcag-taaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaac-----caacgctctc-----tatttgatgt-ccacag--
|| |||||||||||||| ||||| || ||||| |||||| | | || || || ||||||||||| || |||||||| || || ||||| |||| |||||||| || | | ||| || | | | | || | | | || || |||| | | | |||||||| |
AAACCAGATTATGGTCGCTGTGTTGCTATTGTAGCATCTGCGTCGTTAAGAGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTGgtgggttaacttttaattttacatgtctgcacatatattatcattaataaaaccaggggacaacggcaacagttttgcaaatttttgatgtattgtaacc
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 13
AAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCACCCATTGCAGTTGgtgagtcagtaaaaat--gttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctc-tatttgatgtccacag------------
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AAACCAGACTATGGTCGTTGTGTTGCCATTGTAGCATCTGCATCTCTGAGGGAGATGATAAAACCCGGTGCTTTGGCTATTGTATCACCTATAGTGGTTGgtgggtcatctgctctttgttcgttagccttttgtcatgctcaagaaaaaattgtt-gttattgttgctctagcagttatggaacatcatgtttttgcattMapped 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|124825050|gb|EH909916.1|EH909916EST: TCACCCATTGCAGTTG GTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAG
genomic: TCACCCATTGCAGTTGgtgagtcagt ... atgtccacagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGCCAGATTATGGTCGATGTGTCGCCATTGTCGCATCTTCAGCTTTGAGGGAAATGATAAAACCAGGAGCTTTGGCTATAATATCACCCATTGCAGTTGgtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT