Sequence
atgc intronic sequence ATGC exonic sequenceCAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttcttggctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G38200.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G365185_T01 (Zea mays), 5'ss of exon 4
CAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttcttggctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
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CAATCCAAACTCCTTTACCAGTGCAGATACTGCATATGTTCTTGCTTATTCTGTAATCATGCTCAACACTGATGCTCACAATACTATGGTCAAGGATAAGgtaaacaaa--tgataataagcat--atttgattcaagattagtttatttatgagatttccaatgtgcag----------------------------------------------------------------------------------------------------------------------------
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G092586_T01 (Zea mays), 5'ss of exon 4
CAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttcttggctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
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CAATCCAAATGCTTTTATTAGTGCAGATACAGCATATGTTCTTGCATATTCTGTGATCTTGCTAAACACTGATGCTCATAATCCAATGGTGAAGAACAAGgtatactt-----------atgattttattatcatacg-------------ggaatgtctataaagaaatttagttttttaactctatcaaaggtaatctaagttttcttgtgcag------------------------------------------------------------------------------
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G48200.1 (Glycine max), 5'ss of exon 4
CAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttg-tcttcttgg--ctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
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CAACCCTAGTTCTTTTAGCAGTGCAGATACTGCCTACGTTCTAGCTTACTCTGTGATAATGCTTAATACGGATGCTCATAATAACATGGTGAAAGATAAGgtttgaccttgctgaatcttttatattatgtcttaggctcaaccgttagagtaccagctttgtga-cattacttga-tgtccaatctaggtgtggtttcatt-----------------------------------------------------------------------------------------------
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G00230.1 (Glycine max), 5'ss of exon 5
CAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttcttggctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
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CAACCCTAGTTCTTTTAGCAGTGCAGATACTGCCTACGTTCTTGCTTACTCTGTGATAATGCTTAATACAGATGCTCATAATAATATGGTGAAAGATAAGgtttgacctt---gctga-atcttttatatgatgtcttaggctcaacagttagagtac-cagctttgtgaca--ttacttgatgtccaatctagttgtagtttcgtt---------------------------------------------------------------------------------------
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv03s0038g04090.t01 (Vitis vinifera), 5'ss of exon 4
CAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttcttggctgtcacaatt-tattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
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CAATCCAAATTCATTTACCAGTGCTGATACTGCTTATGTTCTTGCTTACTCTGTGATATTGCTGAACACGGATGCCCACAATAACATGGTGAAAGATAAGgtgagcttggagaattttcttatttgtcttctaccccacactta-ggcttacaagtcatgcctttgtgcctaatgtttgtagattagttttttaaggggga----------------------------------------------------------------------------------------------
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S264_74V6.1 (Physcomitrella patens), 5'ss of exon 5
CAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttcttggctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
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CAATCCGAAGGCATTCAGCAGTGCAGATACAGCTTACGTTCTTGCTTACTCTGTGATCATGCTCAATACTGATGCTCACAACCCCATGGTCAAGACCAAGgtcagtgatct-----gttgcaatt---tcacactgcg---------ttcaagtgtgcatatttttgctctgagttct---gctgatcctagacttttacgatatactttggccttttcc--------------------------------------------------------------------------
upper sequence: AT4G38200.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S11_55V6.1 (Physcomitrella patens), 5'ss of exon 5
CAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttcttggctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaactt-ttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
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CAATCCGAAGGCCTTCAGTAGTGCAGATACAGCATACGTGCTTGCTTACTCTGTGATCATGCTTAACACCGATGCCCACAACCCTATGGTCAAAACTAAGgtcagtaatat-----gttagaatc-gcgcattgcgtgagtacgggt-----gcgtgtgcgtgtgtgtattgctttgctcttggttctgttgctcttacattgttgcgtta------------------------------------------------------------------------------------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|116440756|gb|EG483348.1|EG483348EST: CTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAG ATGACCAAGGCTGATTTTATCAGAAATAACCGAGGCATTGATGATGGCAAA
genomic: CTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttc ... tgacaatcagATGACCAAGGCTGATTTTATCAGAAATAACCGAGGCATTGATGATGGCAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAATCCAAATTCATTCAGCAGTGCTGACACAGCATATGTTCTTGCATACTCTGTAATAATGCTTAACACTGATGCCCACAATATCATGGTTAAAGAGAAGgtttgtcttcttggctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA