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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactatgcaccgcgaagcctctggtcctgactagtacggttcttaatctttgcgcgtaacgtttgtctacttgcaattccag

Basic information

species Zea mays
transcript GRMZM2G153977_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153977_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 12
TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactatgcaccgcgaagcctctggtcctg-actagtacggttcttaatctttgcgcgt--aacgtttgtcta------cttgcaattc-cag
|| ||||||||||| |||||||||   ||||||||||||||||||||||||||||| ||||||||||| || || ||||| || |||||||||| |||||||   | || ||  ||     | | |   |   ||     ||||  |   |   |  |||| ||       | | |||||  |||
TATATTCTGAAGGTTGGTGAAGGAGCTGCTGCCCAGTGCATCAGTGGATTCACAGCCATGGACATCCCTCCTCCCCGTGGTCCTCTCTGgtaaa-ctatgcatttccaaacccttgaattagcagtgaaataatttcacttcttgtcatttttgatctttgactgatgcaccctacaatttgcag
















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|108823997|gb|EC278005.1|EC278005
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|211422086|gb|FL442273.1|FL442273
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|60344077|gb|DN211050.1|DN211050
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|67016864|gb|CO445613.1|CO445613
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|60339829|gb|DN206802.1|DN206802
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|37392368|gb|CF633433.1|CF633433
EST:     CACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: CACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|211224716|gb|FL222434.1|FL222434
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|47962710|gb|CN845419.1|CN845419
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|60352456|gb|DN219429.1|DN219429
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|211287001|gb|FL447773.1|FL447773
EST:     TCAGTGGATTCACAGCTATGGACATCCCACCAACCTGGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: TCAGTGGATTCACAGCTATGGACATCCCACC-ACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|211420574|gb|FL478622.1|FL478622
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACYTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|78120564|gb|DV538948.1|DV538948
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|16927203|gb|BM080272.1|BM080272
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|31405529|gb|CD484261.1|CD484261
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|67015196|gb|CO443945.1|CO443945
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|32867897|gb|CF007579.1|CF007579
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|60354188|gb|DN221161.1|DN221161
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|60344368|gb|DN211341.1|DN211341
EST:     ATCAGTGGATTCACTGCTATGGACATCCCACCACCTAGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|33942544|gb|CF349144.1|CF349144
EST:     ATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|32834942|gb|CD974620.1|CD974620
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|60396263|gb|DN229132.1|DN229132
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|60343342|gb|DN210315.1|DN210315
EST:     CTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
genomic: CTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGG
EST: gi|110519064|gb|EE023651.1|EE023651
EST:     ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTG                         GATTCCTGGGCGATGTTTTCATGGGGAGTCTACCACCCCGTCTTCGATTAC
genomic: ATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGA-TCCTGGGCGATGTTTTCAT-GGGAGTCTACCACACCGTCTTCGATTAC

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: 426

TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGGCAAGCTGAGGGTTGGCTTCGCGGAGTCGGCCTAAGGAACGTATGGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 833

TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGGCAAGCTGAGGGTTGGCTTCGCGGAGTCGGCCTAAGGAACGTATGGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1022

TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGGCAAGCTGAGGGTTGGCTTCGCGGAGTCGGCCTAAGGAACGTATGGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 848

TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactat ... gcaattccagGATCCTGGGCGATGTTTTCATGGGAGTCTACCACACCGTCTTCGATTACGGCAAGCTGAGGGTTGGCTTCGCGGAGTCGGCCTAAGGAACGTATGGTTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACATTCTGAAGGTCGGTGAAGGACAAGCTGCCCAGTGCATCAGTGGATTCACAGCTATGGACATCCCACCACCTCGTGGCCCCCTCTGgtaaaactatgcaccgcgaagcctctggtcctgactagtacggttcttaatctttgcgcgtaacgtttgtctacttgcaattccag

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