Sequence
atgc intronic sequence ATGC exonic sequence...aaggatttatttttacctgatgtaccatctgttgagatgcttagtgtaacttttttgctccttttcattgtattgtacgtccgattctttacttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTGTCACTCTGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G043862_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g57210.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------aaggatttatttttacctgatgtaccat-ctgttgagatgcttag----tgtaacttt-tttgctccttttcattgtattgtacgtccgattctttacttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTGTCACTCTGATG
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gttctaaaacttcaacagtacaacttgcttatttcgtctgattaatcttgccttagctaccacatatttgtccagaatggatcttttatgttcctgaaaggattttcttttgtgtcggtattggattaattcaattcgattgtaccatgaaaacttgacttctacagGATGCAAGTAAAGCCTTCTACTCAACCAATTATTGTTGTTCTTCCACTCTGCCACTCGGATGMapped 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|32942378|gb|CF047197.1|CF047197EST: GCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAG GATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTG
genomic: GCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAGgtttgaaact ... acttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTG
EST:
gi|211322504|gb|FL455349.1|FL455349EST: GCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAG GATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTG
genomic: GCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAGgtttgaaact ... acttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTG
EST:
gi|32826199|gb|CD965877.1|CD965877EST: GCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAG GATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGCTGTCCTTCCACTGTG
genomic: GCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAGgtttgaaact ... acttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTG
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:
50GAATTCGGTAACATTGAAGCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAGgtttgaaact ... acttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTGTCACTCTGATG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
141GAATTCGGTAACATTGAAGCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAGgtttgaaact ... acttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTGTCACTCTGATG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
101GAATTCGGTAACATTGAAGCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAGgtttgaaact ... acttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTGTCACTCTGATG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
108GAATTCGGTAACATTGAAGCACCTATGTATGCAAGGCTTCGTCACTTCTTCTCTACAATATATACGAGgtttgaaact ... acttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTGTCACTCTGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaacttttttgctccttttcattgtattgtacgtccgattctttacttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTGTCACTCTGATG
gtgtaac putative branch site (score: 108)
ttctttacttttac putative PPT
attctttactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaggatttatttttacctgatgtaccatctgttgagatgcttagtgtaacttttttgctccttttcattgtattgtacgtccgattctttacttttacagGATGCAAATAAAGCCTTCGACTCAGCCAGTTATTGTTGTCCTTCCACTGTGTCACTCTGATG
- - - - - - - -cctgatg
- - - - - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - - - - - atgctta