Sequence
atgc intronic sequence ATGC exonic sequenceAATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17800.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA01G36880.4 (Glycine max), 5'ss of exon 1
AATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
||||||||||| |||||||| ||||| ||||| ||||| || || ||||| || |||||||||||||| ||||| |||||||||||||||||||| || || |||||| || | || | || | | || || | |||||| | | ||| |||| ||| | ||| | ||
GATGAGCGCTTCTAGGTTCATCAAGTGCGTCACTGTTGGGGATGGTGCTGTGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtacttcctttctcccttctaaaaacataattt------tgggttctgggt-----aattgttctattccgcaatttatgaag--aaattcagctgcatt-tgcatttca-------------------------------------------------------------------------------
upper sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G08380.1 (Glycine max), 5'ss of exon 2
AATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
||||||||||| |||||||| ||||| ||||| ||||| || || ||||| || |||||||| ||||| ||||| ||||||||||||||||| || || || | || || | || | ||| || |||||| | | | | | ||| | | | |||| | | | | | | ||| | |
GATGAGCGCTTCTAGGTTCATCAAGTGCGTCACTGTTGGGGATGGTGCTGTGGGCAAAACCTGCTTGCTTATTTCCTACACCAGCAACACTTTCCCCACCgttagttcttttctctctcctaaaaactaaattttgggttctgggtaattc----tccaattccgcatatt---ttgaataaattcagctacgtttgcatttaatct--------------------------------------------------------------------------------------
upper sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G05160.1 (Glycine max), 5'ss of exon 1
AATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
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-ATGAGCGCTTCTAAGTTCATCAAGTGTGTCACTGTTGGGGATGGAGCTGTGGGCAAAACTTGTTTGCTAATCTCCTACACCAGCAACACCTTCCCCACTgt-ta--gttcttttcttcctcttattttgtttctgtgtattagtgataat--gttttttttttaattttccttttttggaatggattttagagttttggattta----------------------------------------------------------------------------------------
upper sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G23340.1 (Glycine max), 5'ss of exon 1
AATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
||||||||||| |||||||| ||||||||||| || || || ||||| || || ||||| |||||||| || || |||||||||||||| || || || || || |||| || || | | |||| ||| | | | | |||| || | || ||| | | || || | | ||||| ||| || | ||
-ATGAGCGCTTCTAGGTTCATCAAGTGTGTCACTGTCGGGGATGGAGCCGTGGGCAAAACTTGTTTGCTAATCTCCTACACCAGCAACACCTTCCCCACTgt-ta--gttcttttattcctctttttttgtttctttgtg-tattagtgacaatttttttatttcccttttttg--gaatgc--attttagagctt-tgg--atttaaaaa----------------------------------------------------------------------------------
upper sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ04304 (Selaginella moellendorffii), 5'ss of exon 1
AATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
|||||| |||| ||||| || || |||||||| || || || || || || || ||||| || |||| ||||||||||| ||||||||||||||||| | | | || ||| | || || | | | |||||| | | ||
-ATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTAC--Tgtgagattttttcttctctttagatgggaattctaa--ccgtgaatgtctgattccag-------------------------------------------------------------------------------------------------------------------------------------
upper sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ16760 (Selaginella moellendorffii), 5'ss of exon 1
AATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
|||||| |||| ||||| || || |||||||| || || || || || || || ||||| || |||| ||||||||||| ||||||||||||||||| | | | || ||| | || || | | | |||||| | | ||
GATGAGCACTTCCAGGTTTATTAAATGTGTCACTGTGGGAGATGGGGCCGTCGGCAAAACATGCATGCTAATTTCTTACACAAGCAACACTTTTCCTAC--Tgtgagattttttcttctctttagatgggaattctaa--ccgtgaatgtctgattccag-------------------------------------------------------------------------------------------------------------------------------------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|125199253|gb|EL214207.1|EL214207EST: CACCAGCAACACTTTTCCTACG GATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAAT
genomic: CACCAGCAACACTTTTCCTACGgtataatgtt ... tgtggaacagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAAT
EST:
gi|164209962|gb|ES063772.1|ES063772EST: GCAACACTTTTCCTACG GATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAAT
genomic: GCAACACTTTTCCTACGgtataatgtt ... tgtggaacagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATGAGCGCTTCGAGGTTCATAAAGTGTGTCACCGTTGGCGACGGAGCTGTTGGTAAAACCTGTTTGCTGATTTCTTACACCAGCAACACTTTTCCTACGgtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT