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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttcatgttaatctatttgtcaatcattctgttgaacttctattagagatgacacacatgtcgacatcctctgctgttacag

Basic information

species Zea mays
transcript GRMZM2G303655_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 18
GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttcatgttaatctatttgtcaatcattctgttgaac------------ttctattaga-------gatgacacacatgtcgacatcctctgctgttacag
||  |  | || ||||||||||||||||||||||| || || ||||| |||||||| || ||||||||  |||| |||||||| |||  |||| | |  |  || |||||||  ||| ||| || |  ||             || ||  | |        | ||| ||| ||  ||  || | |  |  |||||
GATCTGCGGCCCATTCGTCCACCTGAGAAGAGCAAGGAGGATATACTACTTTTCTTTAAACTTTATAACCCTGAAAAGGAAGAACTTTGgtatatattttcata-tctattttgcaagcatcctttaaaaaaaattagtacaattttaaaaaattagtacaaagactcacgtggtgaagtcattttgttgtacag

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT5G06600.3 (Arabidopsis thaliana), 5'ss of exon 18
GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgta------tgtttcatgttaat----ctatttgtcaatcat-tctgttgaacttctattag--agatgacacacatgtcgacatcctctgctgttacag
|| ||| |||| |||| ||| ||||| ||    |||||||| || ||||||||||||||||||||| |  | ||||||| ||   |   |||      |||| | | ||| |    |  | || |  | || |   |||  || | | ||   |  | ||| | ||  |   |      | | || |  
GATTTACGTCCTATTCCTCCTCCTGAAAAATCAAAAGAAGATATTCTTCTTTTCTTCAAGCTTTATGACCCCGAGAAGGCAGTATTAAGgtagtattgtgttccctcttatttattccctctggcttttatataaattggtctaccactacttaagtaacaaatattccacaagaacgaggtctttctt

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 18
GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttcatgttaatctatt--tgtcaatcattctgttgaacttctattagagatgacacacatgtcgacatcctctgctgttacag
||  |  |||| |||| ||||||||| || |  |||||||| || || |||||||||||||||||| |  ||||||| |||||||| | |||   || || ||| ||  ||      | | | ||| |     ||||    |   |   ||  |  |     | |||   | || |||
GATCTGCGTCCTATTCCTCCACCTGAAAAAACTAAAGAAGATATTCTGCTTTTCTTCAAGCTTTATGACCCTGAGAAAGAAGAGCTCCGgtactattaat-ttattcccttaacactatttactctatgctctttcttcctgctctttgacgtaaat-----ttctcccattttccag

upper sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 18
GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtat----gtttcatgttaatctatttgtcaatcattctgttgaacttctattagagatgacacaca--tgtcgacatcctctgctgttacag----------------------------------
|| |||   ||||  | ||||||||||||||  || || || ||  | |||||||||||||||||| || ||||||||||||||||  ||||      |||   |||  | | ||| |   |   | | | |    |  ||||    | |        ||| ||  || |   ||||||                                     
GATTTACACCCAAACCCTCCACCTGAGAAGACAAAGGATGATATTTTGCTTTTCTTCAAGCTTTATGATCCTGAGAAGGAAGAGCTAAAgtaatcaaattttcagttgctttttttcttctttcctttctgggggctggattacctgtcatttgatgttgttgaattcattacctgttatttgatgttgttgaattcatctcatctgtgatctcag

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|211181104|gb|FL329890.1|FL329890
EST:     GACATACTTNTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCA                         TTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCNTCTGAAATATT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
EST: gi|6536518|gb|AW224831.1|AW224831
EST:     GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCA                         TTTTGNTGGTAGGCTTTTTGCGAAGGCTCTGGGAAAGCCATCTGAAATATT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
EST: gi|211335220|gb|FL322949.1|FL322949
EST:     GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCA                         TTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
EST: gi|211222669|gb|FL338354.1|FL338354
EST:     GACATACTTNTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCA                         TTTTGTTGGNAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
EST: gi|211531762|gb|FL336391.1|FL336391
EST:     GACATACTTCTTTTCTTCAAGCTTTATAATGNTGAGAAGGAAGAGCTTCA                         TTTTGTTGGTANGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
EST: gi|211265134|gb|FL336164.1|FL336164
EST:     GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCA                         TTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGNAAAGCCATCTGAAATATT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
EST: gi|211096696|gb|FL354066.1|FL354066
EST:     GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCA                         TTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCAT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCAT
EST: gi|32935147|gb|CF039959.1|CF039959
EST:     GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCA                         TTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
EST: gi|211148456|gb|FL367819.1|FL367819
EST:     GACATACTTCTTTTCTTCAAGCTTTATA-TGCTGAGAAGGAAGAGCTTCA                         TTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT
genomic: GACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATT

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), 46 (downstream exon)
Score: 244

GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 116

GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 156

GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttca ... gctgttacagTTTTGTTGGTAGGCTTTTTGTGAAGGCTCTGGGAAAGCCATCTGAAATATTGACAAAACTGAATGCAATGGCTGGATTTTCTCCAAATGAAGAAATTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTTATGTCCAATTCGTCCACCTGAGAAGAGCAAAGAAGACATACTTCTTTTCTTCAAGCTTTATAATGCTGAGAAGGAAGAGCTTCAgtatgtttcatgttaatctatttgtcaatcattctgttgaacttctattagagatgacacacatgtcgacatcctctgctgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT