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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcattttttttctgccatgctcctttctgtgttgtctgaaagcattcattgtgattggtttcacttcttttgctaagttttattgtttcttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC

Basic information

species Zea mays
transcript GRMZM2G011101_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g17430.1 (Oryza sativa), 3'ss of exon 2
ctcattttttttctgc-catgctcctttctgtgt-tgtctgaaagcattcattgtgattggtttcacttcttttgctaagttt-tattgtttcttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC
 |  |||| | | |||   ||     |||||| | ||  | | | ||    || || |||   | ||  |||||  ||| |   | ||||| |   | |||||||||||||||||||||| |||||  | |||||||| || ||| |||| || |||||||||||||||||||||||||| ||||||||
-tttttttatgtgtgcatttgtgaacttctgtttgtgcattataacagaagttctggttgtcctaacacctttt--taactcgattttgttaccattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATCATCAAGTCAACAAACATGAAGTGTCTAACACCACC

upper sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G00610.1 (Glycine max), 3'ss of exon 2
---ctcattttttttctgccatgctcctttctgtgttgtctgaaagcattcattgtgattggtttcacttcttttgctaagttttattgtttcttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC
   | ||  | |  |  |   |  |   |   |   |   |    ||||| | ||    || | || ||  ||  | | | |   ||  ||| |   | | |||| || || ||||| ||  | ||||| |||| ||| ||| |||| |||||||||||||| ||||| |||||||| ||||| |||||
aagcacaactgtgatagggattcttgagtcaggcaatacatttctgcattaactg--gctgatatctctgattc-gtttattaaaatgatttttatgttttagGTTGCCGTAAATACAGTATTACAAGATGAGAGGGACTTCCTGAACCACATTATCAAGTCTACAAATATGAAGTGCCTGACTCCACC
















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|5901212|gb|AW042312.1|AW042312
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGGGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|74236156|gb|DT644070.1|DT644070
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|78179458|gb|DV549831.1|DV549831
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|211489682|gb|FL122965.1|FL122965
EST:     CTGATGTTACTTTCCGGAACATGTGGGCASAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|84976649|gb|DW475071.1|DW475071
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|33093348|gb|CF053342.1|CF053342
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|32929197|gb|CF034009.1|CF034009
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|24934221|gb|CA452439.1|CA452439
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|149076797|gb|EE165446.2|EE165446
EST:     AATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
genomic: AATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|60341135|gb|DN208108.1|DN208108
EST:     ACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
genomic: ACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|6827494|gb|AW331137.1|AW331137
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|33094919|gb|CF054913.1|CF054913
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATACTGTGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT
EST: gi|32790600|gb|CD942836.1|CD942836
EST:     CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAG                         GTGGCAGTGAATCCTGTGATTCAGGATGAGAAGGAATTCTTGAATCACATT
genomic: CTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATT

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: 47 (upstream exon), 49 (downstream exon)
Score: 157

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACCTGTGCTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 202

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACCTGTGCTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACCTGTGCTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 196

AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACCTGTGCTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgct ... ttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattgtgattggtttcacttcttttgctaagttttattgtttcttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC
                                 ttttattgtttctt  CT-rich tract
                             taagttttattgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcattttttttctgccatgctcctttctgtgttgtctgaaagcattcattgtgattggtttcacttcttttgctaagttttattgtttcttgttatcagGTGGCAGTGAATACTGTGATTCAAGACGAGAAGGAATTCTTGAATCACATTATCAAGTCAACAAACATGAAGTGTCTGACACCACC

- - - - - ttctgcc
- - - - - - - - - tgctcct
- - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - tgtgatt