Sequence
atgc intronic sequence ATGC exonic sequencegtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
gtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
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gtatgcatttttatttttatgatttataacctattacaaa--atggagaaccagtgaac---aataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------gtatgcctctt--tct---ctttatggctaatagccaatttgaaataatactagatgagggtcctcgaa-tggcgactgatttcaactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATT-GCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
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gtatttgctgacgctaaaccctcgcagcattgtgaagcatgttcgatcgaataccttgcaatctgagcttcattcttgtaggaaaacaaaacattttgctgatctagttctctcttgctaaaaagtaacctttgtgacctttg--tgcagTTGGAGGTCTCCTGAATGCAACTTTTGGAAATGCAACTGAAATGATTATTTGTATCATG-GCCCTGCGGAAGAATATGATACGAGTTGTACAGTTATCACT
upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
----gtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgattt-caactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCAT-TGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
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taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcc-tatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCAT-TGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ12361 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
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---------------gtaataaattatacccttttctcgatcaca----aagagagt----gaatgg----tcctttttgtttctct----tgcagTCGGTGGCCTTCTGAATGCGACGTTTGGAAATGCCACCGAGATGATTATCTCTATCTTCGCTCTGCGGAATGGCATGATCCGCGTGGTTCAGCTGTCGCT
upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ33760 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
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---------------gtaataaattatacccttttctcgatcaca----aagagagt----gaatgg----tcttttttgtttctct----tgcagTCGGTGGCCTTCTGAATGCGACGTTTGGAAATGCCACCGAGATGATTATCTCTATCTTCGCTCTGCGGAATGGCATGATCCGCGTGGTTCAGCTGTCGCTMapped 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|71769706|gb|DR967643.1|DR967643EST: GCAGCTTGCAATATACACTGGTCCAACAG TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST:
gi|149075133|gb|EE163627.2|EE163627EST: GCAGCTTGCAATATACACTGGTCCAACAG TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST:
gi|149072532|gb|EE160814.2|EE160814EST: GCAGCTTGCAATATACACTGGTTCAACAG TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST:
gi|89760510|gb|DY688889.1|DY688889EST: GCAGCTTGCAATATACACTGGTCCAACAG TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST:
gi|60339318|gb|DN206291.1|DN206291EST: GCAGCTTGCAATATACACTGGTCCAACAG TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST:
gi|149085154|gb|EE174658.2|EE174658EST: GCAGCTTGCAATATACACTGGTCCAACAG TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 4 RNA-Seq libraries.
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
51GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
Block sizes:
32 (upstream exon),
49 (downstream exon)
Score:
108GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
Block sizes:
42 (upstream exon),
47 (downstream exon)
Score:
89GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
Block sizes:
29 (upstream exon),
49 (downstream exon)
Score:
135GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
gactgat putative branch site (score: 135)
ctttcct putative PPT
atttcaa TA-rich tract