Sequence
atgc intronic sequence ATGC exonic sequencegtgagagaatcttagtccatgagatttctttgtcgatcatataaactcagaaacgttgttgacagtgttggtttgatgatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGGACTTTGAATCAATCGAAGAAGATAAGCGAAGAGCTATTTGCGAGAGAAGTGCACTCGAGTTTGCGAAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G49820.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 5
---------------gtgagagaatctt------agtccatgagatttctttgtcgatcatataaactcagaaacgttgttgacagtgttggtttgatgatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGGACTTTGAATCAATCGAAGAAGATAAGCGAAGAGCTATTTGCGAGAGAAGTGCACTCGAGTTTGCGAAGATG
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ttcatgagctgattagtgttaccatcttcacaaaagaacatgaaaatccttatt---ttgggtggaatggctaacacttgcatca-tacttatttgat----tggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGCTGCTAAACGGGCTAGTTGTGAACGGCGGGCACTTGATTTAGCTAAGATG
upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G40730.1 (Glycine max), 3'ss of exon 5
---------------gtgagagaatctt------agtccatgagatttctttgtcgatcatataaactcagaaacgttgttgacagtgttggtttgatgatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGGACTTTGAATCAATCGAAGAAGATAAGCGAAGAGCTATTTGCGAGAGAAGTGCACTCGAGTTTGCGAAGATG
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ttcatgagctgattcgtgttaccatcttcacaaaagaacatgaaaatccttatt---ttaggtggaatggctaatacttgcatcatcatta-tttgat----tggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTACTGATGCTGCTAAACGGGCAAGTTGTGAACGGCGGGCACTTGATTTAGCTAAGATG
upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0091g00100.t01 (Vitis vinifera), 3'ss of exon 5
---------------gtgagagaatcttagtccatgagatttctttgtcgatcatataaactcagaaacgttgttgacagtgttggtttgatgatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGGACTTTGAATCAATCGAAGAAGATAAGCGAAGAGCTATTTGCGAGAGAAGTGCACTCGAGTTTGCGAAGATG
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atttatgtaagtggtatcatgaaaccctgtttcttgcattcttgtcatagacttcatacaatta--attttttttaagacttctctatctttggattcacagGAGAATTGTTGGTGTAGCACATGTTGAGGATTTTGAATCAATTGTTGATGCTAGCAAGCGAGCTAACTGTGAGAGACAGGCACTTGTATTTGCAAAGATG
upper sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 5
------------gtgagagaatcttagtccatgagatttctttgtc---gatcatataaactcagaaacgttgttgacagtgttggtttgatgatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGGACTTTGAATCAATCGAAGAAGATAAGCGAAGAGCTATTTGCGAGAGAAGTGCACTCGAGTTTGCGAAGATG
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cgatttatataagtggtatcatgaagccctgtgttacattcttgtcatagacttcatacaattatctctttttaagact-tatcgatcttttgat-tcacagGAGAATTGTTGGTGTAGCACATGTTGAGGATTTTGAATCAATTGTTGATGCTAGCAAGCGAGCTAACTGTGAGAGACAGGCACTTGTATTTGCAAAGATGMapped 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|164142565|gb|ES212613.1|ES212613EST: AGGAATTTGTTGCATGACTCACTCGGATTCGGCGCTGCAAAGATGATTAG GAGAATTGTAGGAGTGGCACATGTTGAGG
genomic: AGGAATTTGTTGCATGACTCACTCGGATTCGGCGCTGCAAAGATGATTAGgtgagagaat ... gatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGG
EST:
gi|116447257|gb|EG489849.1|EG489849EST: AGGAATTTGTTGCATGACTCACTCGGATTCGGCGCTGCAAAGATGATTAG GAGAATTGTGGGAGTGGCACATG
genomic: AGGAATTTGTTGCATGACTCACTCGGATTCGGCGCTGCAAAGATGATTAGgtgagagaat ... gatatggcagGAGAATTGTGGGAGTGGCACATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgatcatataaactcagaaacgttgttgacagtgttggtttgatgatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGGACTTTGAATCAATCGAAGAAGATAAGCGAAGAGCTATTTGCGAGAGAAGTGCACTCGAGTTTGCGAAGATG
atataaact 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagagaatcttagtccatgagatttctttgtcgatcatataaactcagaaacgttgttgacagtgttggtttgatgatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGGACTTTGAATCAATCGAAGAAGATAAGCGAAGAGCTATTTGCGAGAGAAGTGCACTCGAGTTTGCGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG