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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtcacttttgtatggtatagtgttttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcag

Basic information

species Zea mays
transcript GRMZM2G408989_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408989_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 4
GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtcactttt-gtatggtatagtgttttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcag
||||||||| ||||||||||| |||||||||||||||||||| ||||| |||||||| |||||||||||||||||||||      |   | ||||| |   || |  |||||||  |  | | |  |||  |  || |  | | | ||| |||||| |||
GGCCTACCGTGCATTTTACATCCTAAACTGGATTTACCGTTACTTCACTGAGGGTCACCACAGCAGATGGATCCgtaagcgcctgcccctcgtatgcttgtgtttcatatcccatgttctatatatgaaaagaagttc--tgacgatctgtttcttccag

upper sequence: GRMZM2G408989_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv10s0003g01700.t01 (Vitis vinifera), 5'ss of exon 4
GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc---acttttgtatggtatagtgttttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcag---
|||||| || ||||| ||||| || |||||||||||||||||||||||||||   |||   ||| |||||||  |||||||||    |   ||  |  |   |   |||| |        ||    ||    | ||| || |   |  | |  ||  || |    
GGCCTATCGTGCATTATACATCCTCAACTGGATTTACCGTTATTTCACGGAGCAACATTTTAGCCGATGGATAGgtaagttgtgtcaataattaaaaagagcaacatttttttgtggccattgatgcatgtattctgaccgcatctttttttctttgtttatcag
















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|18169894|gb|BM339734.1|BM339734
EST:     CACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: CACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|16920990|gb|BM074929.1|BM074929
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|91871430|gb|EB401416.1|EB401416
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|91871428|gb|EB401415.1|EB401415
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|78023775|gb|DV492162.1|DV492162
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|78023788|gb|DV492175.1|DV492175
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|50330722|gb|CO525848.1|CO525848
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGNCAA-CAGCTCTGTATGCAGATTTCTTTTAC
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTG-CAAACAGCTCTGTATGCAGATTTCTTTTAC
EST: gi|16922820|gb|BM075812.1|BM075812
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|6022165|gb|AW067093.1|AW067093
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|60344375|gb|DN211348.1|DN211348
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|14245658|gb|BG874240.1|BG874240
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|78080743|gb|DV509155.1|DV509155
EST:     GTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: GTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|211107178|gb|FL251311.1|FL251311
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|24769505|gb|CA404634.1|CA404634
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|31354771|gb|CD439128.1|CD439128
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|32912106|gb|CF016918.1|CF016918
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|60342889|gb|DN209862.1|DN209862
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|211379193|gb|FL377345.1|FL377345
EST:     CTGGATTTTACCNGT-ATTTCAAGGNAGGGTCATCACAGCAGATGGATCC                         CTTGGNCTTGGCTGGTTTTGTGCAAACAGCTCT
genomic: CTGGATTT-ACC-GTTATTTCACGG-AGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGG-CTTG-CTGGTTTGGTGCAAACAGCTCT
EST: gi|18169973|gb|BM339813.1|BM339813
EST:     TCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: TCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|18165355|gb|BM335194.1|BM335194
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|78080744|gb|DV509156.1|DV509156
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT

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), 46 (downstream exon)
Score: 24

GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 37

GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 28

GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 33

GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCTACCGGGCATTTTACATTCTAAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtcacttttgtatggtatagtgttttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA