Sequence
atgc intronic sequence ATGC exonic sequence...ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatcagaggtgaaaaaaaaatgactgacaatgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g36890.1 (Oryza sativa), 3'ss of exon 2
ccaaaccttctttactgttcgagttactagt-aacattgcttgcttcatcagaggtgaaaaaaaaatgactgacaa-tgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
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ctataggagtagtag-attcaggtggtaaaagagaatttgcagttgcaacaatgcaggaaaaaaaataaaaggtaactgacactcagacgcacg-tacacagGTGGTCGGCGATCGCGACGCACCTGCCGAAGCGGACGGACAACGAGATCAAGAACTACTGGAACACGCACCTGAAGAAGAGGCTCGCCAGGATGGGCATC
upper sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S389_40V6.1 (Physcomitrella patens), 3'ss of exon 1
ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatca-gaggtgaaaaaaaaatgactgacaatgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
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tttgttttgttttgtttttttgtgtttttttgtgtgtgtgtgcgagtgcgtggagcacagaaaaattgattttttggaatgtgttgttgt-tgattcgcagATGGTCTGCCATAGCTAGCCATCTTCCTCGCCGCACTGACAACGAGATCAAGAACTACTGGAACACACACTTGAAGAAGCGTCTCATGCAAATGGGAATT
upper sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S106_216V6.1 (Physcomitrella patens), 3'ss of exon 2
---ccaaaccttctttac----tgttcgagttactagt-------aacattgcttgcttcatcagaggtgaaaaaaaaatgactgac-aatgacatgccc----tcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
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gtactgaattttcttcccgtcgcgttgggatgtctcatttctgcagacgtcgcgcg-ttggttacactccacaaaattgtcagttcctaacagcatttctcgtttcttgattgcattagATGGTCAGCCATCGCGGGCCATCTCCCCCAGCGTACAGACAACGAGATAAAGAACTACTGGAACACGCATTTGAAGAAACGTTTGGCACAGATGGGAATC
upper sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 2
-ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatcagaggtgaaaaaaaaatgactgacaatgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
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ttgaaattttacttctttttgtaacagttaggactagt-tatcttgaataccatttttttaatatatcgctttcttatttatttatttatttatattgtagGTGGTCAGCCATAGCAAGCCATCTTCCCCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACGCACTTGAGGAAGCGACTGCTGCAAATGGGGATT
upper sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatcagaggtgaaaaaaaaatgact--gacaatgacat--gccctcgcgcaaccc--gcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
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gtgatgcctctaactgttataaaaccctctaattctgatccttctgtaacattgttggtgcgatcgtcttggcggtgttttcatgacgctttcgacgcg-aagttccatgtggta--gccttcttttgtaacaatgcggacctagtgttttgaacgatggctctggttattgtgttttttttgcagATGGTCAGCTATAGCTAGTCATCTTCCTCGCCGCACTGACAACGAGATAAAAAACTACTGGAACACTCACTTGAAGAAGCGTCTGCTGCAAATGGGGATT
upper sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ18722 (Selaginella moellendorffii), 3'ss of exon 1
ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatcagaggtgaaaaaaaaatgactgacaatgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
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--------------------gtgaaaccggtaaca--gtttgtagagttttacctctaaattctgcgttctctaagttcttgcgt--gtttcactttcagGTTGTCCGTGATCGCATCGCACATTCCTGGACGAATTGACAACGAGATTAAAAACCACTGGAACACACACCTCAAGAAG---------------------
upper sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ18565 (Selaginella moellendorffii), 3'ss of exon 1
ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatcagaggtgaaaaaaaaatgactgacaatgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
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-----------------------------gtaaca--gtttgtagagttttacctctaaattcttgcgttctctaagctct-tgcgtgtttcactttcagGTGGTCCGTGATCGCATCGCACATTCCTGGACGAACTGACAACAAGATTAAAAACTACTGGAACACACACCTCAAGAAGCAATTGTTGCAAATGGGAATC
upper sequence: GRMZM2G001223_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ18723 (Selaginella moellendorffii), 3'ss of exon 2
ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatcagaggtgaaaaaaaaatgactgacaatgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
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-----------------------------------------------gtaagagtttgtagagttttacctctaagttcttgcgtttctc--actttcagGTGGTCCGTGATCGCATCGCACATTCCTGGACGAACTGACAACGAGATTAAAAACCACTGGAACACACACCTCAAGAAGCAATTGTTACAGATGGGGATTMapped 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|89252337|gb|DY624123.1|DY624123EST: TGCAGGAGGAGCAGGACCATCATCCAGCTCCACGCTCTCCTCGGCAACAG GTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAA
genomic: TGCAGGAGGAGCA-GACCATCATCCAGCTCCACGCTCTCCTCGGCAACAGgtgatcattc ... caacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAA
EST:
gi|148964775|gb|EC906032.2|EC906032EST: CTGCAGGAGGAGCAGACCATCATCCAGCTCCACGCTCTCCTCGGCAACAG GTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAA
genomic: CTGCAGGAGGAGCAGACCATCATCCAGCTCCACGCTCTCCTCGGCAACAGgtgatcattc ... caacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcagaggtgaaaaaaaaatgactgacaatgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
gactgac putative branch site (score: 2)
tgaaaaaaaaatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaaaccttctttactgttcgagttactagtaacattgcttgcttcatcagaggtgaaaaaaaaatgactgacaatgacatgccctcgcgcaacccgcagGTGGTCGTCGATCGCGACGCACCTGCCCAAGCGCACGGACAACGAGATCAAGAACTACTGGAACACGCACCTCAAGAAGCGGCTCGCCAAGATGGGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - tttactg
- - - - - - - - - - - - - - - - - -ttgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgccc