Sequence
atgc intronic sequence ATGC exonic sequence...tttagaaagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccacacatccttatgccataaaacgaatttcctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 3'ss of exon 12
tttagaaagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccacacatccttatgccataaaacgaatttc--ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
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tacaagtacagaaccattatgtta-agcaatactttattactctcagaatagtgattttgcagttgtt-ttgtgcgataacataatttttttctgctgtcagGCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAG
upper sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA20G02950.2 (Glycine max), 3'ss of exon 10
---------------------------------------------------tttaga-aagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccac-acatccttatgccataaaacgaatttcctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
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gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaataaaataaaaaaagtgcaagcgtcaattggtggaaacaaagttctatttccccccctctaaaaaggtaaataattcaatttccttctttttaacagGAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAG
upper sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G35090.1 (Glycine max), 3'ss of exon 13
------------------------------------------tttagaaagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccacacatccttatgccataaaacgaatttcctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
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gtaaggttttagtaactagttgataatttttgttagggtgcttttcttcagtataaaaaagtgcaagcgtcaattggtgaaaacaaagttctatttcccccctctaaaaaggcaaataattcgatttccttcttttttacagGAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAG
upper sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 12
lower sequence: Vv06s0004g00140.t01 (Vitis vinifera), 3'ss of exon 12
tttagaaagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccac-acatccttatgccataaaacgaatttcctatcatc-------agGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
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-----gacctgtttttcctacat---gtctttttcttgaaagttgcatgttttctttcgtcttgatttgcttactgagcattttctttctttcattatctgcaaatagGCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGMapped 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|211117707|gb|FL407753.1|FL407753EST: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG GCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
EST:
gi|67012552|gb|CO441301.1|CO441301EST: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG GCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
EST:
gi|32834869|gb|CD974547.1|CD974547EST: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG GCGGTGGGACAAATTTGAAGATTCGTAC
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTAC
EST:
gi|211410948|gb|FL407147.1|FL407147EST: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG GCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
EST:
gi|60340979|gb|DN207952.1|DN207952EST: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG GCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
EST:
gi|211337107|gb|FL422018.1|FL422018EST: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGG GCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
genomic: GCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGG
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),
48 (downstream exon)
Score:
114GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
Block sizes:
47 (upstream exon),
48 (downstream exon)
Score:
78GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
125GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
154GTATACTTACAAGGTCTGTGCATATAAGAAAGCATCACAGGCTGAAGGGCACAGTTCTACCAACCTGGGgtatgcttat ... ctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtatgttttttccccacacatccttatgccataaaacgaatttcctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
tttcctatc CT-rich tract
tttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagaaagtggatttcagtgatagaataacttgcttgaatgttcggtatgttttttccccacacatccttatgccataaaacgaatttcctatcatcagGCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacgaa