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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttctttgctaataaatactacacttgtgttacttgtacataaaatggctggcatacatctgcagttcctttgttcttaatttcttttgctcctacattctggttctgggtaaacttatataacgtaatctgaaaatgccctatttgtttctcaaatttttcag

Basic information

species Zea mays
transcript GRMZM2G013625_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013625_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g47262.2 (Oryza sativa), 5'ss of exon 8
GTTATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttctttg--ctaataaatactacacttgtgttacttgtacataaaatggctggcatacatctgcagttcctttgttcttaatttcttttgctcctacattctggttctgggtaaacttatataacgtaatctgaaaatgccctatttgtttctcaaatttttcag
||||||||||||||||| ||||| |||||| | || ||||| ||||| || |||||||| |||| ||  |   |  | | |     | | ||| |  |   |    | | |||    |     || ||  ||    ||||   |    |||   | |  ||   | ||                                                         
GTTATGTTACCAGAGGCCGTTGCGATTGTGATTGCTCCCACTGATCCTACTAGgcaagtattctatggacggttgtacagtttcaatttattattccttt-tgcttttggtggtgccccctgccaatttattatcacttacagtgaaatgcatatgctctcaaatcctttag-----------------------------------------------------
















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|78086947|gb|DV515340.1|DV515340
EST:     ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
EST: gi|78115431|gb|DV533819.1|DV533819
EST:     ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
EST: gi|71328261|gb|DR800761.1|DR800761
EST:     ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
EST: gi|71426234|gb|DR807284.1|DR807284
EST:     ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
EST: gi|71767635|gb|DR965572.1|DR965572
EST:     TGTTACCAGAGGCTGTTGTCA-TTGTGGTCGCACCCACAGATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAA
genomic: TGTTACCAGAGGCTGTTG-CAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAA
EST: gi|32795556|gb|CD947792.1|CD947792
EST:     GATCCCACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: GATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
EST: gi|32795393|gb|CD947629.1|CD947629
EST:     GATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: GATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
EST: gi|18168836|gb|BM338676.1|BM338676
EST:     GGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: GGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
EST: gi|76014394|gb|DT941564.1|DT941564
EST:     ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
EST: gi|37375435|gb|CF624155.1|CF624155
EST:     ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAG                         GAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG
genomic: ATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAG

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), 48 (downstream exon)
Score: 51

GTTATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAGGGAGTGTGACGAAAGTGGGTTCCACACTCACCGAGAGACAACCAACGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 122

GTTATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAGGGAGTGTGACGAAAGTGGGTTCCACACTCACCGAGAGACAACCAACGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

GTTATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAGGGAGTGTGACGAAAGTGGGTTCCACACTCACCGAGAGACAACCAACGGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 101

GTTATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttc ... aatttttcagGAGTTACGGAATATTCAGGCTGACTGAACCTGGAGGGATGGATGTTCTTAGGGAGTGTGACGAAAGTGGGTTCCACACTCACCGAGAGACAACCAACGGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATGTTACCAGAGGCTGTTGCAATTGTGGTCGCACCCACAGATCCAACCAGgcaagtgttctttgctaataaatactacacttgtgttacttgtacataaaatggctggcatacatctgcagttcctttgttcttaatttcttttgctcctacattctggttctgggtaaacttatataacgtaatctgaaaatgccctatttgtttctcaaatttttcag

- - - - - - -  GCTGTT