Sequence
atgc intronic sequence ATGC exonic sequencegtgagctatttgatttctacatgcagaacttctatcctttgattgcatagattactgatatgtactgctgaaacattaaaacggctttctgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 13
gtgagcta-tttgatttctacatgcagaacttctatcctttgattgcatagattactgatatgtactgc-tgaaacattaaaacggctttctgtttat--cagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
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gtgagcttcttctacatgtacatgtaaacattgt-ccgttaagttgtttgaat-----atat-tacagcataggttatgaagattgctattgaaatattgcagGTTTATTGACAATTGGCCCCCGTTTTGGTGGTGCAATTGATGATGCTGCCCGGTACTTCAAAGATGCATATGATAGA
upper sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G49460.1 (Arabidopsis thaliana), 3'ss of exon 13
gtgagctatttgatttctacatgcagaacttctatcctttgattgcatagattactgatatgtactgctgaaacatt----aaaacggctttctgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
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-----------------gtcagtcaacattttttttcccccacaaaacacataagttctctttaccgtccaacaatctctaagaatgttaaaccataaaacagGTTTATTGACCATTGGTCCCCGATTTGGTGGTGCCATTGATGACGCTGCTCGATACTTCAAAGACGCGTGTGACAGG
upper sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0077g00950.t01 (Vitis vinifera), 3'ss of exon 13
----------gtgagc-tatttgatttctacatgca--gaacttctatcctttgattgcatagattactgatatgtactgctgaaacattaaaacggctttctgttt--atcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
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gtaaattgtagcaattatgtttcatttttatttagatggagggatcatatcttcattggaaatgctg-tagtgtgggcttttg------tgaactgattttataatggaaacagGCTTGCTTACAATTGGTCCCCGATTTGGTGGAGCTATTGATGATGCTGCTCGATACTTCAAGGACGCTTATGATAGG
upper sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
------------gtgagctatttgatttctacatgcagaacttc---tatcctttg--attgc-atagattactgatatgtact-gctgaaacattaaaacggctttctgttt-----------atcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG-----------------------
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gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
upper sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ31368 (Selaginella moellendorffii), 3'ss of exon 12
gtgagctatttgatttctacatgcagaacttctatcctttgattgcatagattactgatatgtactgctgaaacattaaaacggctttctgtttat-cagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
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----------------------------------------gttcgtgtgactccttcatttgtattttt-----------acaactatttgcttgtgcagGCCTTCTTACAATAGGACCTCGTTTTGGCGGAGCTATTGATGATGCAGCCCGCTACTTCAAAGATGCTTACGACAAG
upper sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ06573 (Selaginella moellendorffii), 3'ss of exon 12
gtgagctatttgatttctacatgcagaacttctatcctttgattgcatagattactgatatgtactgctgaaacattaaaacggctttctgtttat-cagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
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-----------------------------------------------------gttcgtgtg-actccatcggtatttttacaactattttcttgtgcagGCCTTCTTACAATAGGACCTCGTTTTGGCGGAGCTATTGATGATGCAGCCCGCTACTTCAAAGATGCTTACGACAAGMapped 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|60401030|gb|DN233837.1|DN233837EST: ACCTTGTTTCCAGCTTGGTGTCTG GATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCC
genomic: ACCTTGTTTCCAGCTTGGTGTCTGgtgagctatt ... tgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCC
EST:
gi|32931181|gb|CF035993.1|CF035993EST: TATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTG GATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCC
genomic: TATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTGgtgagctatt ... tgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCC
EST:
gi|211308719|gb|FL364517.1|FL364517EST: TATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTG GATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCC
genomic: TATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTGgtgagctatt ... tgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCC
EST:
gi|78116146|gb|DV534534.1|DV534534EST: TATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTG GATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCC
genomic: TATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTGgtgagctatt ... tgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCC
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:
49 (upstream exon),
49 (downstream exon)
Score:
80ATCATGCTTTGTGCGGACCATGGTCCCTGTGTATCTGGTGCTCATAACTCTATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTGgtgagctatt ... tgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
101ATCATGCTTTGTGCGGACCATGGTCCCTGTGTATCTGGTGCTCATAACTCTATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTGgtgagctatt ... tgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
110ATCATGCTTTGTGCGGACCATGGTCCCTGTGTATCTGGTGCTCATAACTCTATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTGgtgagctatt ... tgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
379ATCATGCTTTGTGCGGACCATGGTCCCTGTGTATCTGGTGCTCATAACTCTATAGTTACTGCTAGGGCTGGAAAGGACCTTGTTTCCAGCTTGGTGTCTGgtgagctatt ... tgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatagattactgatatgtactgctgaaacattaaaacggctttctgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
tactgat putative branch site (score: 379)
ctttctgttt putative PPT
aaacattaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctatttgatttctacatgcagaacttctatcctttgattgcatagattactgatatgtactgctgaaacattaaaacggctttctgtttatcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG