Sequence
atgc intronic sequence ATGC exonic sequence...cgtgcattggaagccggtatttgctagttgtttctctctctctctttttcttttaggtgcgcgcctgccaactaaattgtgtttctcttgtctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 1
---cgtgcattggaagccggtatttgctagttgtttctctctctctctttttcttttaggtgcgcgcctgccaactaaattgtgtttctcttgtctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
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taacaagtattggaatcttgtgtat--tagaagacaccatcctttagatagtttattca-tgtacttttgccactgaaattgtgccttccttgtaattggcagATGCCGGGAGAAGCAGCGCAAGGAGGCCTCCCGGCTGCAAACTGTGAACCGGAAGCTGAATGCGATGAACAAGCTGTTGATGGAGGAAAATGACCGGCTG
upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------------------------------------cgtgcattggaagccggtatttgctagttgtttctctctctctctttttcttttaggtgcgcgcctgccaactaaattgtgtttctcttgtctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
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gtgtctttcttttcaaaatttcaaataacccaaatgccaaaatctcccatttcttattcttcctcaaaaaaagccttcaacttcacctattttttttatcttgtctcaatgaaagaacgcaactttttttagttcctattttgtgtttctttttattgttcttagaaggcattggtgaattttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGCTTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTGTTAATGGAGGAGAATGACCGTTTG
upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 1
cgtgcattgga-agccggtatttgctagttgtttctctctctctctttttcttttaggtgcgcg--cctgccaactaaattgtgtttctcttgtctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
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---gaaatgaataatgaatgactatcatacaatgttatggtaaattgtatgggaaagatgacctactctacctgccttatactctgccaattttcttctgtagATGTCGTGAAAAGCAGCGGAAGGAAGCCTCTCGTCTGCAGACAGTGAATAGAAAGCTGTCTTCAATGAACAAGTTGTTAATGGAAGAGAACGACCGACTG
upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 1
---cgtgcattggaagccggtatttgctagttgtttctctctctctctttttcttttaggtgcgcgcctgccaactaaattgtgtttctcttgtctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
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acttgagagagtgaaatgaataatgaatgactataatacaatgttatggtaaattctatgggaaagattacctact---ctacctgccaattttcttctgtagATGTCGTGAAAAGCAGCGGAAGGAAGCCTCTCGTCTGCAGACAGTGAATAGAAAGCTGTCTGCAATGAACAAGTTGTTGATGGAAGAGAACGACCGACTG
upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 1
cgtgcattggaagccggtatttgctagttgtttctctctctctctttttcttttaggtgcgcgcctgccaactaaattgtgtttctcttgtc--tttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
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cttctgttc-atttttctattatttcaacacatttatcatactgctataggtttgtctttaacttttctggtttcttt-tggttgttttgttgactttttagATGTCGAGAGAAGCAGAGGAAAGAGTCAGCTCGTCTTCAGACAGTGAACAGGAAGCTGAGTGCTATGAACAAGCTTTTGATGGAAGAGAATGATCGTTTG
upper sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 1
cgtgcattggaagccggtatttgct--agttgtttctctctctctctttttcttttaggtgcgcgcctgccaactaaattgt--gtttctcttgtctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
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----tgattatagcttctattccattcagtcttgaggaaaaatttagtgatggctgatgagctactatctcaacccatgtgtttgctctttttctgtttaatagGTGCCGTGAAAAGCAAAGGAAGGAAGCTTCTCGTCTCCAGACTGTGAATCGGAAGTTGACTGCAATGAACAAGCTGTTGATGGAAGAGAATGACCGGTTAMapped 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|211094381|gb|FL362905.1|FL362905EST: CTCACCAACGTCGAGCCCAGGCAGATCAAGGTCTGGTTCCAGAACCGCAG ATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCG
genomic: CTCACCAACGTCGAGCCCAGGCAGATCAAGGTCTGGTTCCAGAACCGCAGgtcagtcgcc ... tctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcttttaggtgcgcgcctgccaactaaattgtgtttctcttgtctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
aactaaa putative branch site (score: 2)
tgtttctcttgtcttt putative PPT
aactaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgtgcattggaagccggtatttgctagttgtttctctctctctctttttcttttaggtgcgcgcctgccaactaaattgtgtttctcttgtctttggtagATGCCGGGAGAAGCAGCGGAGGGAGTCCTCTCGTCTGCAGACCGTCAACCGGAAGCTGGGTGCCATGAACAAGCTGTTGATGGAGGAGAACGACCGGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
-gtgcatt
- - - - - - - - - - -tgctagt
- - - - - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaa