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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatctcacctcagtatcataacttgttcgaacttgtaaaagatactagtttgtccgttgctagttggatgggcaatatactaacttcatggcgtgaaattctgggcattaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTC

Basic information

species Zea mays
transcript GRMZM2G159388_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159388_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g12650.1 (Oryza sativa), 3'ss of exon 2
gtaaga---tctcacctcagtatcataacttgttcgaacttgtaaaagatactagtttgtccgttgctagttggatgggcaatatactaacttcatggcgtgaaattctgggcattaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTC
||||||   | |  | ||  ||||| ||||||||| |  ||    ||   |  |   ||| |      || | |||    | || |  ||    | | |   ||| | ||  | ||  |||||| |||| ||   ||||||||||||||| ||||| |||||||| |||||||||||||| ||||| || ||||| ||||||||||| |||||||||||||| 
gtaagattgtttttcatctctatcacaacttgttcaagttttggcaaagcataatcatgttccac---aggtagata---attacataaa----aggtctctaaactgtgccctttctttcagGTCTCCCCCGCGGATCCCAGAGGTGATTATTCCAGAAGATTTGGTTGTCAACATTGCTCTATCTACACGTTATGAGATCAACAGGGCCTTTGCCAATCTT
















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|60395326|gb|DN228195.1|DN228195
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|37377979|gb|CF625638.1|CF625638
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCAACGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|71319886|gb|DR796701.1|DR796701
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|213170374|gb|FM192501.1|FM192501
EST:     CTCTGGTCC-ATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: CTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|29946755|gb|CB816309.1|CB816309
EST:     GCCCTGGGTGTTCTCTTTCTCTGGGCCAATGCTTCATCGGTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGGGATCATTCCTGAAAGATT-AGTTGTCA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAA-GATTTAGTTGTCA
EST: gi|29576879|gb|CB616991.1|CB616991
EST:     CCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: CCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|211035915|gb|FK990122.1|FK990122
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|76915381|gb|DV165958.1|DV165958
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|22545660|gb|BU098019.1|BU098019
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|60345750|gb|DN212723.1|DN212723
EST:     CCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: CCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|60395367|gb|DN228236.1|DN228236
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|9952806|gb|BE639389.1|BE639389
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAG
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAG
EST: gi|60396494|gb|DN229363.1|DN229363
EST:     CAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: CAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|29544868|gb|CB605476.1|CB605476
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|71319888|gb|DR796702.1|DR796702
EST:     CCCTGAGTGTTCTCTTTCTCT-GTCCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: CCCTGGGTGTTCTCTTTCTCTGGT-CCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|6564128|gb|AW231750.1|AW231750
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|30031743|gb|CB833594.1|CB833594
EST:     GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
EST: gi|67017360|gb|CO446109.1|CO446109
EST:     GTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAA                         GGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA
genomic: GTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAA

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: 641

AATTGCTTGGCTACCATCTCCTTACTTTTGTTTGCCATGGTCTCATATTCGCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 379

AATTGCTTGGCTACCATCTCCTTACTTTTGTTTGCCATGGTCTCATATTCGCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 551

AATTGCTTGGCTACCATCTCCTTACTTTTGTTTGCCATGGTCTCATATTCGCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

AATTGCTTGGCTACCATCTCCTTACTTTTGTTTGCCATGGTCTCATATTCGCCCTGGGTGTTCTCTTTCTCTGGTCCAATGCTTCATCGTTTATCCACAAgtaagatctc ... attaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttggatgggcaatatactaacttcatggcgtgaaattctgggcattaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTC
            aatatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatctcacctcagtatcataacttgttcgaacttgtaaaagatactagtttgtccgttgctagttggatgggcaatatactaacttcatggcgtgaaattctgggcattaattcagGGCTCCACCAAAGATCCCAGAGGTGATCATTCCTGAAGATTTAGTTGTCAACATTGCGCTATCCACTCGTTACGAGATCAACAGAGCCTTTGCCAATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA