Sequence
atgc intronic sequence ATGC exonic sequence...acttaaccaggatcagtattttataaggttcatctgggctttcccccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------------acttaaccaggatcagtattttataaggttcat-ctgggctt---tcccccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtggttg----cagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
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gtgatgattctagggcagttttcttgagatctggtaacctgtgctctttggcttcacttgctcgaagtggtttcctgatgaacatgagagagaatgttgaaaaattcttgctgtgacggggttcaatggattaaagggctctctttttggtgttgagtgacaagaagtttgtggttgatttcagGTTGAATGCACAATTCCGAAAGATGATGGGACTTTAGCATCTTATGTTGGGTTTAGGGTCCAACACGACAATGCTAGGGGACCTATGAAGGGTGGAATCA
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 2
---------------------acttaaccaggatcagtattttataaggttcatctgggctttccccc----ctatccgaaacagtatgttcaacttttgagt--aacaagcagtttgtggt--tgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
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gcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagt-tcaccaactctagttctaaataaatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 1
acttaaccaggatcagtattttataaggttcatctgggctttcccccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
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tcatagttttgttgtgcatactatgtctttaacatatatgatatgcataacatagtttagcaactcctccagttctaaatcttgttgaatgaaaatgcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGATTCAGGATTCAACATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCA
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 1
-------------------acttaaccaggatcagtattttataag-----gttcatctgggctttcccccctatccgaaacagtatgttcaacttttgag-taacaagcagtttgtggt--tgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
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gcaagtaaaattacttcttgtgtttttcatttctttgttctggcaaaattagtttacttgttttcactgtactgtttcatatagt-tcaccaactctagctctaaatcatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACGTTGCAATCTTATGTTGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G16320.1 (Glycine max), 3'ss of exon 2
acttaaccaggatcagtattttataaggttcatctgggctttcccccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtg-gttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA--------------
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--------------------------------------------------------------------------------------gtcagaataatgcatgttgaatgtaccatacctaaacatgatggcacgttgcaatcttatgttgggttcagGGTTCAACATGATAATGGCACAGGCCCCATGAAAGGAGGAATCAGATACCATCCTGAG
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 2
--acttaaccaggatcagtattttataaggttcatctgggctttcccccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
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tgatggcaccttgatggcttctgttttgttcttattttgtatttatcagataagcataaaatgcaactctagttctaa--aacatgttgaatgaaaatgcagGTTGAGTGTACCATCCCCAAAGATGATGGAAGCTTGGCCACTTTTGTTGGATTCAGAGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGGATCA
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 3
acttaaccaggatcagtattttataaggttcatctgggctttcccccctatccgaaacagtatgttcaac----ttttgagtaa--------caagcagtttgtg----gttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
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---------------gtggtttctaatgatatgctcagttttctcatccatg-ataaccgtatgatttaccattttttgactatgctcttttcacttcttttgaacaaaattgcagGTTGAGTGCACCATACCCAAAGACGATGGTACTTTGGCATCATTTGTTGGATTCAGGGTTCAACATGACAATGCTAGAGGCCCCATGAAGGGAGGGATCAMapped 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|20300929|gb|BQ163872.1|BQ163872EST: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST:
gi|20301193|gb|BQ164136.1|BQ164136EST: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
gagtaac putative branch site (score: 2)
aactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttaaccaggatcagtattttataaggttcatctgggctttcccccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA