Sequence
atgc intronic sequence ATGC exonic sequenceCCCGGGAAATCTCTTGACCGGTTTCGGCTTCTATGAGCCATTCTGGCTCGTCGATTTCGCCAACGCTTGCATTGTTCTTCATTTAGTTGGTGGATATCAGgtatctcagaaaccccttgcccatctaaccaacatgctcgttgatttttatgttttcgttcacattttagaaaacaaactaccattctagtattttagac...
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23810.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23810.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os04g39489.1 (Oryza sativa), 5'ss of exon 6
CCCGGGAAATCTCTTGACCGGTTTCGGCTTCTATGAGCCATTCTGGCTCGTCGATTTCGCCAACGCTTGCATTGTTCTTCATTTAGTTGGTGGATATCAGgtat------ctcagaaacccctt--------gcccatctaacc-aacatgctcgttgatttttat--gttttcgttc-acattttagaa----aacaaactaccattctagtattttagac--
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CCCTGGCAACCTCCTCACCGGCTTCGGCTTCTACGAGCCCTACTGGCTCATCGACTTCGCCAACGCCTGCATCATCCTCCACCTGCTCGGCGGCTACCAGgtacacagcaccaagaaaccatttcagtgtgcactgatagaactgaaaataatcctgaaacacaatcagtcactgatcgacattgccggatgatgatgaatgaaaaaaaacttggtttgatcag
upper sequence: AT5G23810.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G155491_T01 (Zea mays), 5'ss of exon 6
CCCGGGAAATCTCTTGACCGGTTTCGGCTTCTATGAGCCATTCTGGCTCGTCGATTTCGCCAACGCTTGCATTGTTCTTCATTTAGTTGGTGGATATCAGgtatctcagaaaccccttgcccatctaaccaacatgctcgttgatttttatgttttcgttcacattttagaaaacaaactaccattctagtattttagac
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GCCGGGCAACCTCCTCACCGGCTTCGGCTTCTACGAGCCGTACTGGCTCATCGACTTCGCCAACGCCTGCATCATCCTCCACCTGCTGGGCGGGTACCAGgt---tagtacgcgcgctgacagt------gaca-gcccgccgaaacacgaatctgaaaccaaaccctgcag----------------------------
upper sequence: AT5G23810.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ29928 (Selaginella moellendorffii), 5'ss of exon 5
CCCGGGAAATCTCTTGACCGGTTTCGGCTTCTATGAGCCATTCTGGCTCGTCGATTTCGCCAACGCTTGCATTGTTCTTCATTTAGTTGGTGGATATCAGgtatctcag--aaaccccttgcccatctaaccaacatgctcgttgatttttatgttttcgttcacattttagaaaacaaactaccattctagtattttagac
|| ||||| ||| | || || || |||||||| ||||| ||||||||| |||||||||| ||||||||||| || | || | || || | || || || | | ||| ||| | | ||| | | |||| || || |||||| || | | | | | ||
TCCTGGAAACCTCCTCACGGGCTTTGGCTTCTACGAGCCCTTCTGGCTCATCGATTTCGCAAACGCTTGCATCGTCATCCACCTTGTAGGAGCGTACCAAgtcggtaaatcaaaacccatctttgatcatccatcttctcaaaaaatttccatcttgtcgttcttatctgtcgtgtctctttcacttcacag----------
upper sequence: AT5G23810.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ25118 (Selaginella moellendorffii), 5'ss of exon 5
CCCGGGAAATCTCTTGACCGGTTTCGGCTTCTATGAGCCATTCTGGCTCGTCGATTTCGCCAACGCTTGCATTGTTCTTCATTTAGTTGGTGGATATCAGgtatctcag--aaaccccttgcccatctaaccaacatgctcgttgatttttatgttttcgttcacattttagaaaacaaactaccattctagtattttagac
|| |||||||| | || || || |||||||| ||||| ||||||||| |||||||||| ||||||||||| || | || | || || | || || || | | ||| ||| | | ||| | | |||| || || |||||| || | | | | | ||
TCCTGGAAATCTTCTCACGGGCTTTGGCTTCTACGAGCCCTTCTGGCTCATCGATTTCGCAAACGCTTGCATCGTCATCCACCTTGTAGGAGCGTACCAAgtcggtaaatcaaaacccatctttgatcatccatcttctcaaaaaatttccatcttgtcgttcttatctgtcgtgtctctttcacttcacag----------Mapped 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|125265335|gb|EL279420.1|EL279420EST: CCAACGCTTGCATTGTTCTTCATTTAGTTGGTGGATATCAG GTATACAGTCAACCAATTTTCGCGGCTGCGGAGAGATCGCTAACCAAGAAA
genomic: CCAACGCTTGCATTGTTCTTCATTTAGTTGGTGGATATCAGgtatctcaga ... gacattttagGTATACAGTCAACCAATTTTCGCGGCTGCGGAGAGATCGCTAACCAAGAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCCGGGAAATCTCTTGACCGGTTTCGGCTTCTATGAGCCATTCTGGCTCGTCGATTTCGCCAACGCTTGCATTGTTCTTCATTTAGTTGGTGGATATCAGgtatctcagaaaccccttgcccatctaaccaacatgctcgttgatttttatgttttcgttcacattttagaaaacaaactaccattctagtattttagac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa