Sequence
atgc intronic sequence ATGC exonic sequence...gatattgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactgatctgttctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g57220.1 (Oryza sativa), 3'ss of exon 4
gatattgtggttatgttccttgagaacagtatgttcaagatagttttgtc-tgtttactgatctgttctgttct--gtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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gtaattatcagcatgacc--tgatttcaacatttt---ggcccttctgtgacacctgatgaattgtgttatcattaattctaacagGTCCTCCTGTCAATTTGTTCACTGCTGACGGACCCGAACCCCGATGATCCGTTGGTGCCGGAGATTGCTCACATGTACAAGACTGATAGGGCCAAGTATG-----------------
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G17800.1 (Glycine max), 3'ss of exon 3
gatattgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactgatctgttctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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-----------------gtaatagaataatttatttaatttaattttgttataatggatacttaaaatgttaaaattttgtagGTTCTTCTGTCTATATGCTCTCTATTGACAGACCCTAACCCAGATGATCCTCTGGTGCCTGAGATTGCTCAAATGTACAAGACTAACAGAGCCAAGTATG-----------------
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G18310.1 (Glycine max), 3'ss of exon 4
---------------gatattgtggtta-tgttccttgagaacagtatgt-tcaagatagttttgtctgtttactgatctgttc-tgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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aatttaacatctaaagaaaatgtgaaagctgtggattagagccgatatttattcaagtattcagacttaattacttaattattaatgcaatttgttg-tagGTGCTACTTTCAATTTGCTCCCTGCTGACAGATCCCAACCCGGATGATCCTTTGGTGCCTGATATTGCTCACATGTACAAGACTGACAGAGACAAGTACG-----------------
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G17760.1 (Glycine max), 3'ss of exon 3
gatattgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactgatctgttctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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-----------------gtaaaagaataatttatttaatttaattttcttgtaatggatacttaaaatgttaaaattgtgtagGTTCTTCTATCTATATGCTCTCTACTAACAGACCCCAACCCAGATGATCCTCTGGTGCCCGAGATTGCTCAAATGTATAAGACTAACAGAACCAAGTATG-----------------
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G35600.1 (Glycine max), 3'ss of exon 3
gatattgtggttatgttccttgagaacagtatgttcaagatagttttgtc-tgtttactgatctgttctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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-gtaatctgatgatgattatt---atttttatttttaaatttttcttgtaatggatact----taaaatgttaaaactttgtagGTCCTCCTGTCTATATGCTCTCTGCTGACAGATCCCAACCCAGATGATCCTCTGGTGCCCGAGATTGCTCACATGTATAAGACTGACAGAGCCAAGTATG-----------------
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G17740.1 (Glycine max), 3'ss of exon 3
gatattgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactgatctgttctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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-----------------gtaacgaaataatttatttaatttaattttcttgtaatggatacttaaaatgttaaaattgtgtagGTTCTTCTATCTATATGCTCTTTGCTGACAGACCCCAACCCAGATGATCCTCTAGTGCCTGAGATTGCTCAAATGTACAAGACTAACAGAGCCAAGTATC-----------------
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: AT5G56150.2 (Arabidopsis thaliana), 3'ss of exon 4
--------gatat-tgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactgatctgtt--------ctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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ctagatttaatttgtttaatgactctcattagcgagacaatgataatcttttatttgcatataagctgaagaactaaagttggtggtgcaatttccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCTTTGGTTCCTGAAATAGCGCACATCTACAAGACAGACCGAGTCAAGTACG-----------------
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0015g01190.t01 (Vitis vinifera), 3'ss of exon 4
------------------gatattgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactg-atctgttctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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ttttatttaccagtgaaagaaacagctgggacatagaggccatttagggtgc-cagaacagtaatgagtttgtgctctgtattttcaatgctg-gcctgcagGTGTTGCTCTCTATATGCTCGCTGCTGACGGATCCAAACCCGGATGATCCCTTGGTGCCAGAAATTGCCCACATGTACAAGACCGACAGAGCCAAATATG-----------------
upper sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
lower sequence: EDO98738 (Chlamydomonas reinhardtii), 3'ss of exon 4
----------gatattgtgg--ttatgttccttgagaacagtatgttcaagatagttt-tgtctgttta--ctgatctgttctgttctgtatta--acaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
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gatcggtccttatcccgcagacctccgctcgctccgccccgccaacgcatgttcgttcgtaccccttcaaccaaaccaacgccgtccttccctgctgcagGTGCTGCTCTCGATCTGCTCCTTGCTCACGGACCCCAACCCCGATGACCCGCTTGTGCCGGAGATCGCGCACATCTACAAGACCGACCGCCGGCGGTACG-----------------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|31628504|gb|CD526640.1|CD526640EST: AGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGCCCTGCTTTAACTAT CTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGC
genomic: AGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATctcaaaggta ... tgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtctgtttactgatctgttctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
tattaac putative branch site (score: 1)
ttctcctgtc putative PPT
tgtattaa 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 |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatattgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactgatctgttctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
- - - - - - -tgttcct
- - - - - - - - - - - - - - - - - - - - - - - - tctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatctg