Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaaagtgggtcggtagttaaaatctgctcgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 4
gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaa-agtgggtcggtagttaaaatctgctcgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
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gtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
upper sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G13080.1 (Glycine max), 3'ss of exon 5
-------------------------------gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaaagtgggtcggtagttaaaatctgctcgat--------ttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
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gtgtgtgatattgtgctactttaagagagatgatgtctatggcatccaactcttcgtaa-tgttaatgatatcactaagag-gtgtatggactaatttttcttttcccttttgtcggtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGTTTTGGTAATCATTACCCAAAACATGTTCACCATAGAGGAGCATCTATAC
upper sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S64_152V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaaagtgggtcggtagt--taaaatctgctc---gattt---gcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
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gttcattttcctaaatcttatccttgtcgtgctcctctagaattcgtcgtattactcggtggagctctggtttttgatgattgtcgtgagtct-tctgtggtcttaacattgagtttgggatctcatgtagGTCGATTACGCGCTTGGAAAGAATCCCTTGAAGACGAGCTACGTTGTGGGATACAGCGAAAAATATCCTTTACAACCTCGTCACCGAGCAGCCTCCATCC
upper sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ37685 (Selaginella moellendorffii), 3'ss of exon 5
gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaaagtgggtcggtagttaaaatctgc-tcgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
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------------------------------gttcgccgcttc-ctctcttatgcttcatatctctcacacgcctttgcctttctccacagGTGGACTACATTCTGGGAAAGAACCCGCGGAAGATGAGCTACGTCGTGGGATACGGCAACAAGTATCCCAAGCAAGTACACCACCGAGCGGCATCCATCC
upper sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ31524 (Selaginella moellendorffii), 3'ss of exon 5
gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaaagtgggtcggtagttaaaatctgctcgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
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------------------------------------------------------gttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTCMapped 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|211308479|gb|FL124617.1|FL124617EST: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG CTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGSTACGTTGTGGGT
genomic: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
EST:
gi|160481653|gb|EY254223.1|EY254223EST: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG CTTGACTACATCCTTGGAAAGAACCCATTGAA
genomic: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAA
EST:
gi|211308480|gb|FL124618.1|FL124618EST: CCCGCA-GTTTGCCCAG-TCACAGN CTTGACTACATCCCTTGGAAAGAACCCATTGAAGATGAGCTTACGTT
genomic: CC-GCAAGTTTGCC-AGGTCACAG-gtaaatcgtt ... cgatttgcagCTTGACTACATCC-TTGGAAAGAACCCATTGAAGATGAGCT-ACGTT
EST:
gi|211308480|gb|FL124618.1|FL124618EST: CCCGCA-GTTTGCCCAG-TCACAGN CTTGACTACATCCCTTGGAAAGAACCCATTGAAGATGAGCTTACGTT
genomic: CC-GCAAGTTTGCC-AGGTCACAG-gtaaatcgtt ... cgatttgcagCTTGACTACATCC-TTGGAAAGAACCCATTGAAGATGAGCT-ACGTT
EST:
gi|74239514|gb|DT647428.1|DT647428EST: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG CTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
EST:
gi|211001820|gb|FL229076.1|FL229076EST: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG CTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
EST:
gi|67010311|gb|CO439060.1|CO439060EST: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAG CTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
genomic: GACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGT
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:
39 (upstream exon),
49 (downstream exon)
Score:
37TTTATACAGCGACTATCTTGAAGCGGCTGACACGCCTGGGTGGTACTGTGGACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
Block sizes:
48 (upstream exon),
47 (downstream exon)
Score:
70TTTATACAGCGACTATCTTGAAGCGGCTGACACGCCTGGGTGGTACTGTGGACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
45TTTATACAGCGACTATCTTGAAGCGGCTGACACGCCTGGGTGGTACTGTGGACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
Block sizes:
45 (upstream exon),
49 (downstream exon)
Score:
189TTTATACAGCGACTATCTTGAAGCGGCTGACACGCCTGGGTGGTACTGTGGACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgtt ... cgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccttacattagcagagaaagtgggtcggtagttaaaatctgctcgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC
accttac putative branch site (score: 189)
tctgctc putative PPT
tagttaaaat TA-rich tract