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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttggtcgttttgttagaatcacaacaaaataaacatatactttgttatcaaattacagcgccctcttgttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG

Basic information

species Zea mays
transcript GRMZM2G138349_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138349_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g10480.1 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------gtaattttggtcgttttgt------tagaatcacaa-caaaataaacatatactttgttatcaaattacagcgccctcttgttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG
                                                     |    ||  |||||||||      | |  || ||  || || |  || | | | |  |   ||||| || |      | | ||  |||||||||| ||||| || || ||||| | ||||||||| ||||||||||| |||||||| |||||||||||||| |||||||| || ||||| || |||
gtagtattatgaaatcctaattttctgatggtttctgggcaactaattcaagatcgaattcatcgttttgtaccacattgtctctcattcagaacatgcagaaattcttgttctaaatttcaccatatcttcgctgtgtgcagAAAGCGCAAACCTCGGTGATCAAAGCCAACCTGAACCCTGTCTGGAACGAAGAACTCAAGCTCTCTGTTCCTCAGCAATACGGCCCTCTCAAACTG

upper sequence: GRMZM2G138349_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------gtaattttggtcgttttgttagaatcacaacaaaataaacat--atactttgttatcaaattacagcgccctcttgt-tgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG
                                                  |  | ||  || |||  ||  |||   |    | || |  |  ||| |||  | ||  | |  |      |  | | ||  | ||||  |  || ||  | ||||| ||  | ||  ||||||| ||||||||||| ||||| | ||| |||||||| ||||||| ||||    ||||  ||
gttggttgttctcagttctcattagcataaattaattcatgggaaacttttgctctttatcttttatttttaattgaagagtagtagatgttgataattttctttctgaattgactttggtgctatatgccttcagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG

upper sequence: GRMZM2G138349_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 5
----------------------------------------gtaattttggtcgttt-tgttagaatcacaacaaaataaacatatactttgtta-tcaaattacagcgcc--ctcttgt----tgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG
                                        | || ||| | | ||| | ||  | |   ||   || |    || | |||| || |    || | |      || | ||    ||  | ||||  |  || ||  | ||||| ||  | ||  ||||||| ||||||||||| ||||| | ||| |||||||| ||||||| ||||    ||||  ||
gttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatcttttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG

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|213172275|gb|FM186438.1|FM186438
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
EST: gi|71768791|gb|DR966728.1|DR966728
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAAC
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAAC
EST: gi|78179014|gb|DV549387.1|DV549387
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
EST: gi|50334442|gb|CO529568.1|CO529568
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
EST: gi|12046228|gb|BF728367.1|BF728367
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
EST: gi|211245510|gb|FK953342.1|FK953342
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
EST: gi|6918414|gb|AW399944.1|AW399944
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
EST: gi|78087463|gb|DV515856.1|DV515856
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAA
EST: gi|78087464|gb|DV515857.1|DV515857
EST:     GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAG                         AAAGCACAAACTTCAGTAAATCA-TGGCAACCTGAATCCTGTCTGGAATGA
genomic: GGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAA-TCAATGGCAACCTGAATCCTGTCTGGAATGA

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), 47 (downstream exon)
Score: 126

CATTGGAATATTGAATGTCAAGGTGATTGGAGGCACCAACCTAGCCATCAGGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 330

CATTGGAATATTGAATGTCAAGGTGATTGGAGGCACCAACCTAGCCATCAGGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 128

CATTGGAATATTGAATGTCAAGGTGATTGGAGGCACCAACCTAGCCATCAGGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 342

CATTGGAATATTGAATGTCAAGGTGATTGGAGGCACCAACCTAGCCATCAGGGATATGTCAAGCAGTGACCCTTATGTCGTCCTGACACTTGGGCAACAGgtaattttgg ... ttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaataaacatatactttgttatcaaattacagcgccctcttgttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG
                                           tgttgat  putative branch site (score: 342)
                                     ccctcttgtt  CT-rich tract
     ataaacatatactttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttggtcgttttgttagaatcacaacaaaataaacatatactttgttatcaaattacagcgccctcttgttgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG