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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggaacttatcttctctcctcacaatgatcttagcctagttatatcaagaaacaactaaacctctgtgctgtactgcatttctttgtactagagttatcaatcacaactttatttgttatgtttatcaaaaatataaaattgttaattgattttcttctgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG

Basic information

species Zea mays
transcript GRMZM2G038848_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 4
gtgggaacttatcttctctcctcacaatgatcttagcctagttatatcaagaaacaactaaacctctgtgctgtactgcatttctttgtactagagttatcaatcacaactttatttgttatgtttatcaaaaatataaaattgttaattgattttcttctgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG
                                                                    |   ||| | ||||| ||| || |||| ||      |   | | || |  || || | ||||||| | ||| | | |    || || |||| |||| |||||||||| || |   | || ||||||||||| || || |||||| |||||||||| |||||||| |||||||||||||| |||||||||
--------------------------------------------------------------------tttggtagtacatttatttttattagaatttctgggccatattgtagtcattttgctgatcaaaattgtaagactct--gctggttatcttttgatatgcagGACCTCCCAAATTTAGTTGCAATAAAAGATGCAGATTTTTCAAATGTTGATGCGGTTTTTTGTTGCTTGCCACATGGAACAACCCAG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 4
gtgggaacttatcttctctcctcacaatgatcttagcctagttatatcaagaaacaactaaacctctgtgctgtactgcatttctttgtactagagttatcaatcacaactttatttgttatgtttatcaaaaatataaaattgttaattgattttcttctgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG
                                            ||  |          || |||  ||||     |  || | || ||  || |   |   ||     | | | || ||  | |  |||||| | |   ||  |   |||||  |||| |    ||||||||||||| |   | || ||| ||||||| || || |||||| |||| ||||| |||||||| ||||||||||||||||||||||||
-------------------------------------------gtaagatctttttctcaatccttggtgcataggtaaatgttttggtggtacatacaattattgtgccataaattttt--gctggtcaaaactgttggataat--gttgatgctcttttttcatgcagGACCTGCCAAATTTAGTTGCAGTAAAAGATGCAGATTTTTCAAATGTGGATGCAGTTTTTTGTTGCTTGCCACATGGTACAACCCAG
















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|78093374|gb|DV521748.1|DV521748
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|31354246|gb|CD438603.1|CD438603
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|211345290|gb|FL126063.1|FL126063
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCCATAAAAGACGCTGAC
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGAC
EST: gi|211345286|gb|FL126059.1|FL126059
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|148943028|gb|EC888078.2|EC888078
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|148946776|gb|EC892045.2|EC892045
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|211345285|gb|FL126058.1|FL126058
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGA
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGA
EST: gi|89757643|gb|DY687157.1|DY687157
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|148942779|gb|EC887806.2|EC887806
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|71429367|gb|DR810417.1|DR810417
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|30705270|gb|CD058727.1|CD058727
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|91878697|gb|EB408654.1|EB408654
EST:     AAAAGCTGGCGAGCAATTTGGATCAGTATTTCCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: AAAAGCTGGCGAGCAATTTGGATCAGTATTTCC-TCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|148946555|gb|EC884293.2|EC884293
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|211345293|gb|FL126066.1|FL126066
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTKATAACACAG                         GAACCTGCCGAGACTGGTCGCAATAAAAGAMGCTGACTTTTCAGATGTTGA
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGA-CCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGA
EST: gi|78080160|gb|DV508572.1|DV508572
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|78079274|gb|DV507686.1|DV507686
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|74234671|gb|DT642585.1|DT642585
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
EST: gi|149074521|gb|EE162917.2|EE162917
EST:     GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAG                         GACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT
genomic: GAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGAT

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: 105

GATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

GATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

GATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 45

GATTCTAGCGAACCACCCTCAGTTTCATATAAAAGTGATGACTGCAGATAGAAAAGCTGGCGAGCAATTTGGATCAGTATTTCCTCACTTGATAACACAGgtgggaactt ... tgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttatgtttatcaaaaatataaaattgttaattgattttcttctgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG
                                          ttctgat  putative branch site (score: 45)
                                     ttttcttctgattt  CT-rich tract
     atgtttatcaaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggaacttatcttctctcctcacaatgatcttagcctagttatatcaagaaacaactaaacctctgtgctgtactgcatttctttgtactagagttatcaatcacaactttatttgttatgtttatcaaaaatataaaattgttaattgattttcttctgatttgcagGACCTGCCGAGACTGGTCGCAATAAAAGACGCTGACTTTTCAGATGTTGATGCTGTTTTTTGCTGCTTGCCACATGGTACAACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT