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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcattgtcttctccgcatttttgtttctttttaagtgttttgtgtcatcattctttaggctattatcatctgccaccctttgtgttgtaccatt...

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 5'ss of exon 8
AAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcattgtcttctccgcatttttgtttctttttaagtgttttgtgtcatcat--tctttaggctattatcatctgccaccctttgtgttgtaccatt
| |||||||| ||||| ||||| ||||| ||||| |||||||| |||||||| || || || || |||||||| || ||||||||||| |||||||| |||| ||     | |  || |   |||         | ||   |   |     |||  |  || ||  |  |||| |||  |  ||  |   ||||      | 
AGAAGATATACCCAAGCGATGGCTTACTCCCTATATACATAAACCCTCATTCAGGAACTGCGTCGTACTCAACAATTACATTTGGTGCAATGGGAGATAGgttatacttctattctcact-tattcaaacaagctatttccttcctgaaaacatagtggtccttctgtgattaacattagt-actttccatgttaatttgtg
















Mapped 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|67028781|gb|CO457530.1|CO457530
EST:     TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAG                         CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
genomic: TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
EST: gi|60349712|gb|DN216685.1|DN216685
EST:     TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAG                         CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
genomic: TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
EST: gi|22543150|gb|BU093588.1|BU093588
EST:     TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAG                         CTTCTACGAATATTTGCTCAAGGNCTGGATCCAGGGGAATAAAACTGAGCA
genomic: TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
EST: gi|32849483|gb|CD989164.1|CD989164
EST:     TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAG                         CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
genomic: TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
EST: gi|22935539|gb|BU571814.1|BU571814
EST:     TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAG                         CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
genomic: TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
EST: gi|60342116|gb|DN209089.1|DN209089
EST:     TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAG                         CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
genomic: TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
EST: gi|32941898|gb|CF046717.1|CF046717
EST:     TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAG                         CTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA
genomic: TCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCA

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: 187

AAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 145

AAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 202

AAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 353

AAAAGATATATCCAAGTGATGGTTTACTGCCTATTTACATAAATCCTCATTCTGGGACAGCATCATACTCAACTATCACATTTGGTGCTATGGGAGACAGgtaatgtcat ... ttctgttcagCTTCTACGAATATTTGCTCAAGGTCTGGATCCAGGGGAATAAAACTGAGCATGTAAAACACTACAG