Sequence
atgc intronic sequence ATGC exonic sequence...atgccttttactactgagatgacttttttactgtaaccgatttgcttgttgattcccctttccccactgtcaatttagtggctatttgttgattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 3'ss of exon 1
atgccttttactactgag-atgacttttttactgta-accgatttgcttgttgattcccctttccccactgtcaatttagtggctatttgttgattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
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-ttctgcttgagggtgtgcaaagcatatttgatgtgtaaaagtttgcttgcttggcgcattgatgggtcgaccaacaaactgatgatt-atcaatgtggcagGTGGTAAGGATGGTTGTCAGCACTTACCAAGCAGCAAGTGGTGCTGGGGCTGCGGCCATGGAAGAACTCAAACTTCAAACTCAAGAG
upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G05250.1 (Glycine max), 3'ss of exon 1
atgccttttactactgagatgacttttttactgtaaccgatttgcttgttgattcccctttccccactgtcaatttagtggctatttgttgattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
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--------------gtccatcattgcctttccaaattcttccaaattataattactattatctgtggtgtgacgcc--tttctgcttcaatattgcacagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCTAGTGGTGCGGGTGCTGCTGCAATGGAAGAGCTTCAGCTGCAAACTCGTGAG
upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 1
atgccttttactactgagatgacttttttactgtaaccgatttgcttgttgattcccctttccccactgtcaatttagtggctatttgtt--gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
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ccgcaattagaagcttagacactagtttatttataatgcaaatttttat-gttttgtgtttgtatgct-ttggtgtgatgcctttctgcttgaatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG
upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 3'ss of exon 1
---atgccttttactactgagatgacttttttactgtaaccgatttgcttgttgattcccctttccccactgtcaatttagtggctatttgttgattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
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gccaggccagttgcccaagtgtcttggggtttacttgggccatcatg-tagttttggctgaacgctttacgatcgtgct--tcattgtatgtgaatgttttagGTAGTACGCATGGTTGTCAGCACATATCAGGCAGCTAGTGGTGCTGGTGCTGCTGCAATGGAGGAGCTTGAACTGCAAACTCGTGAGMapped 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|18964615|gb|BM661107.1|BM661107EST: CGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAG GTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCT
genomic: CGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAGgtaccacttt ... gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCT
EST:
gi|7216942|gb|AW563049.1|AW563049EST: CGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAG GTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCT
genomic: CGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAGgtaccacttt ... gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCT
EST:
gi|7216973|gb|AW563095.1|AW563095EST: CCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAG GTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCT
genomic: CCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAGgtaccacttt ... gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCT
EST:
gi|60343769|gb|DN210742.1|DN210742EST: CGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAG GTGTTAAGGATGGTTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGC
genomic: CGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAGgtaccacttt ... gattcggcagGTGTTAAGGATGGTT-GTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGC
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:
45 (upstream exon),
49 (downstream exon)
Score:
121GGCGAACGTCCGCCTCGGGCAGGGGGCGATTGTGGCAAATCCGAATTGCTCGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAGgtaccacttt ... gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
128GGCGAACGTCCGCCTCGGGCAGGGGGCGATTGTGGCAAATCCGAATTGCTCGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAGgtaccacttt ... gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
158GGCGAACGTCCGCCTCGGGCAGGGGGCGATTGTGGCAAATCCGAATTGCTCGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAGgtaccacttt ... gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
Block sizes:
45 (upstream exon),
49 (downstream exon)
Score:
64GGCGAACGTCCGCCTCGGGCAGGGGGCGATTGTGGCAAATCCGAATTGCTCGACCATCATCTGCCTCATGGCTGCCACGCCGCTCCATCGCCACGCTAAGgtaccacttt ... gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgattcccctttccccactgtcaatttagtggctatttgttgattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
tgttgat putative branch site (score: 64)
tcaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgccttttactactgagatgacttttttactgtaaccgatttgcttgttgattcccctttccccactgtcaatttagtggctatttgttgattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-tgccttt
- - - - - ctactga
- - - - - - - - - - - - - tttactg