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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttggatgaccatgtattctgaaatagttgatttaactcgcattgggcatgccaatacattcagcaaattttgtctataactgaatgtgtctggactctggaatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT

Basic information

species Zea mays
transcript GRMZM2G063792_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 3
gtcagtttggatgaccatgtattctgaaatag------ttgatttaactcgcattgggcatgcc-aatacattcagcaaattttgtctat---aactgaatgtgtctggactctggaatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT
||||||| |||   |    |    |  ||| |      || | || |   |  |   ||||||  |||   || |   |     || |||   |||||||  | | ||||       ||||| ||||||||||||||||||| ||||| |||||||||| |||||  ||||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||
gtcagttgggagagctgcctccgttagaattgaacatcttaacttgagatgtttcttgcatgctgaatttgttgacagagcggagtatattgaaactgaaactttttggat------atacatcagGTACCTTTGGTCAGGTATTGGAATGTTGGGATAGGGAAAGGAAAGAAATGGTGGCCATTAAGATCATCAGAGGCATTAAGAAGTACAGGGATGCTGCAAT

upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 3
gtcagtttggatgaccatgtattctgaaatagttgatttaactcgcattgggcatgccaatacattcagcaaattttgtctataactgaatgtgtctggactctggaatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT
||  ||||      || |  |   |    ||   |    |  |   |||  ||| ||  ||   || ||    |    ||| |  ||  || |   |    | ||   | |  ||||||||||||||||||| ||||| || ||||||| ||||||||| || ||||| || |||||  |  |  | || || || || ||  | || || |||||
gtttgtttatgcaccccttcaagtttctttaagcggcagagttta-atttagca-gcatatttctttagatgttgcattcttttgctacatattctt----tttg---ttctacagGTACCTTTGGTCAGGTTTTGGAATGCTGGGATAGGGAAACAAAGGAGATGGTTGCTATAAAAGTTGTTCGAGGTATCAAAAAATATCGTGAGGCAGCAAT
















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|211184127|gb|FL126415.1|FL126415
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GTACCTTTGGTCACGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
EST: gi|6020972|gb|AW065900.1|AW065900
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
EST: gi|211186529|gb|FL126424.1|FL126424
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GTACCTTTGGTCAGGTGTTGGAGTGTTGGGATA
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATA
EST: gi|18650268|gb|BM499087.1|BM499087
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
EST: gi|211186533|gb|FL126428.1|FL126428
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACWAAAGAA-TGG
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
EST: gi|211184126|gb|FL126414.1|FL126414
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGG
EST: gi|211186527|gb|FL126422.1|FL126422
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGA
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGA
EST: gi|211186523|gb|FL126418.1|FL126418
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GGTACCTTTGG-CAGGTGTTGGAGTGTTGGGGATAAGGAAACAAAAGAAAT
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagG-TACCTTTGGTCAGGTGTTGGAGTGTTGGG-ATAAGGAAACAAAAGAAAT
EST: gi|211186534|gb|FL126429.1|FL126429
EST:     ATAAGATCAATGCAAAAATGGGAGAAG                         GTACCCTTTGGTCAGGTGTTTGGAGTGTTGGGGATAAGGAAACAAAAGAAA
genomic: ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACC-TTTGGTCAGGTGTT-GGAGTGTTGGG-ATAAGGAAACAAAAGAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 208

ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 191

ATAAGATCAATGCAAAAATGGGAGAAGgtcagtttgg ... aatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattcagcaaattttgtctataactgaatgtgtctggactctggaatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT
                  ctataac  putative branch site (score: 191)
         aaattttgtctataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtttggatgaccatgtattctgaaatagttgatttaactcgcattgggcatgccaatacattcagcaaattttgtctataactgaatgtgtctggactctggaatacaccagGTACCTTTGGTCAGGTGTTGGAGTGTTGGGATAAGGAAACAAAAGAAATGGTGGCCATAAAGATCATCAGGGGCATTAAGAAGTACAGGGATGCTGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC