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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGGTTCATCAATTTTGACAGCACTGTCATCATGGATGTGTAAACCAGGGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttttaaattaccttttcctgacctatgttgtgcatttagaacccagcatcatatgtttcttttgttctttacag

Basic information

species Zea mays
transcript GRMZM2G142502_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142502_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g39660.2 (Oryza sativa), 5'ss of exon 5
AACTGGTTCATCAATTTTGACAGCACTGTCATCATGGATGTGTAAACCAGGGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttttaaattaccttttcctgacctatgttgtgcatttagaacccagcatcatat----gtttc-ttttgttctttacag
 |||||| | || |||||  ||||||||||  ||||||||||||| || ||||||||||| || ||  |  |||||||||||||||||| | | ||||||||||||||||| |  ||  || |||||  |||   | |  |  ||  |   ||  ||||||    | ||| ||||   |  || ||
CACTGGTCCTTCCATTTTAGCAGCACTGTCCACATGGATGTGTAAGCCGGGGTATGCTTCATTACCGCTGCCATATGCCAGAGCTGGCAATCAACTTCTGgtaaggtttttgacctaaattatcctgctctaccatataaacctattatt-agtctcatatctaagcttcattttacccgctatag
















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|78081830|gb|DV510242.1|DV510242
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
EST: gi|71438193|gb|DR819243.1|DR819243
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
EST: gi|149014312|gb|EE043889.2|EE043889
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
EST: gi|148970848|gb|EE021623.2|EE021623
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
EST: gi|89106855|gb|DY577072.1|DY577072
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
EST: gi|22521311|gb|BU080122.1|BU080122
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
EST: gi|89106854|gb|DY577071.1|DY577071
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
EST: gi|148959588|gb|EC905543.2|EC905543
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTNCA-TGCATCTGCCTGTTTCATCGGATGA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTT-CAATGCATCTGCCTGTTTCATCGGATGA
EST: gi|22520755|gb|BU079566.1|BU079566
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
EST: gi|78082996|gb|DV511389.1|DV511389
EST:     GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTG                         GATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA
genomic: GGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAA

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: 279

AACTGGTTCATCAATTTTGACAGCACTGTCATCATGGATGTGTAAACCAGGGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAACTATTTAGTTTGCTCGATGAAGCAAGTGAAAAAACATTTCTTTGCACAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 99

AACTGGTTCATCAATTTTGACAGCACTGTCATCATGGATGTGTAAACCAGGGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAACTATTTAGTTTGCTCGATGAAGCAAGTGAAAAAACATTTCTTTGCACAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 91

AACTGGTTCATCAATTTTGACAGCACTGTCATCATGGATGTGTAAACCAGGGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAACTATTTAGTTTGCTCGATGAAGCAAGTGAAAAAACATTTCTTTGCACAA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 118

AACTGGTTCATCAATTTTGACAGCACTGTCATCATGGATGTGTAAACCAGGGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttt ... ttctttacagGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCCTGTTTCATCGGATGAACTATTTAGTTTGCTCGATGAAGCAAGTGAAAAAACATTTCTTTGCACAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGGTTCATCAATTTTGACAGCACTGTCATCATGGATGTGTAAACCAGGGTATGCTTCGTTGCCAGTTGCATATGCCAGAGCTGGCAGTGAGCTTCTGgtaaggtttttaaattaccttttcctgacctatgttgtgcatttagaacccagcatcatatgtttcttttgttctttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT