Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaactgaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g14810.1 (Oryza sativa), 3'ss of exon 15
gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaact---------gaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
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gtgagtggttatggttttgcagtggtgaatattatt-ttatgagcccaaattttatctgtgtaaatgcaatta-ttttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAG
upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 16
gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaact---------gaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG---------------------
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gtgagtggttatggttttgcagtggtgaatattatt-ttatgagcccaaattttatctgtgtaaatgcaatta-ttttgtcctcggtgcagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTACATTATACTCCATTCATGTATTTCCAATCACAAGAACAGGTAATTGCAAAACTCTAGATG
upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 15
--------gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaactgaatgc--aactaattttgcat-ttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
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gtatgtggtttagtggttacttattgatgaccctgatctctattttatcacattactcttttgatactgaactgtttaaatttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAG
upper sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 15
gtgagtcgctatattttttttatagtgaaaaaaaatgttatggac-accaaactga-atgcaactaattttgcatt--tcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
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gtatgtgcttacttttttatgaccctgatctctattttatcacattactcttttgatattgaactgtttaaattttattattgcagATATGCTGATATTTATACATCTAGGGTGTCAAATTTTTTGTATTATACACCCTTCATGTATTTCCGCTCTCAGGAACAGMapped 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|32834655|gb|CD974333.1|CD974333EST: TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST:
gi|78025583|gb|DV493970.1|DV493970EST: TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST:
gi|5713778|gb|AI943770.1|AI943770EST: TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST:
gi|211089552|gb|FL477198.1|FL477198EST: CCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: -CACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST:
gi|211089553|gb|FL477199.1|FL477199EST: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST:
gi|148967092|gb|EE018262.2|EE018262EST: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST:
gi|12973741|gb|BG268632.1|BG268632EST: TCACGTGCTGGCCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
EST:
gi|16917596|gb|BM073359.1|BM073359EST: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAA ATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
genomic: TCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCC
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:
47 (upstream exon),
49 (downstream exon)
Score:
86ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
133ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
89ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
170ATGGGGTTGGTTGTCACGTGCTGGTCTATGGGATAAGAGTCATCTTACCAGGCAAATTGAAAAgtgagtcgct ... tttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaaatgttatggacaccaaactgaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
aactaat putative branch site (score: 170)
catttcct putative PPT
aactaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcgctatattttttttatagtgaaaaaaaatgttatggacaccaaactgaatgcaactaattttgcatttcctgtagATATGCTGATATATACACATCAAGGGTTTCAAATTTTCTGCACTATACTCCATTCATGTATTTCCAATCTCAAGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC