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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcaactcctacattgatttaatgctctctcttttttcttcttaatccctctgtatgcatcttatctttactcttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCTTTTGGAAAACGGGAGG

Basic information

species Zea mays
transcript GRMZM2G701689_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g41230.2 (Oryza sativa), 3'ss of exon 7
gtttcaactcctacattgatttaatgctctctcttttttcttcttaatccctctgtatgcatcttatctttactcttc----------atcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCTTTTGGAAAACGGGAGG
|||  | ||| ||||  ||  | ||| | |  | || || ||||||  ||||  | ||   ||| |   | ||| |||          || ||||||||||| ||||||||  | |||||| |||| ||||| ||||||||||||||||| |   ||||||
gttctagctcttacac-gaggtcatgatttgacattctt-ttcttagccccttggcatttgtctcactgtcacttttcttaaaaaaaaatgaagGGTGGTGTTGGATGCTCTGTGAGTTGCCGATGTGAGGGTTGTAAGAATGCTTTTGGGAGGAGGGAGG
















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|50331744|gb|CO526870.1|CO526870
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|87156415|gb|DY401204.1|DY401204
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|26559555|gb|CA831790.1|CA831790
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|31359966|gb|CD444323.1|CD444323
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|31349638|gb|CD433995.1|CD433995
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|60394383|gb|DN227253.1|DN227253
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|32932451|gb|CF037263.1|CF037263
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|31357841|gb|CD442198.1|CD442198
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|20512944|gb|BQ280130.1|BQ280130
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|76915167|gb|DV165860.1|DV165860
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|7162203|gb|AW519825.1|AW519825
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
EST: gi|22715536|gb|BU197816.1|BU197816
EST:     GCAATTGCAAGAAGTCGTCATGTCTNNNNNNNTACTGTGAATGTTTTCAG                         GGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT
genomic: GCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCT

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), 48 (downstream exon)
Score: 257

GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCTTTTGGAAAACGGGAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 210

GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCTTTTGGAAAACGGGAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 286

GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCTTTTGGAAAACGGGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

GACTTCTCCAATAAAACTCCTGCTTCAGCTCGTCACAAAAGGGGATGCAATTGCAAGAAGTCGTCATGTCTAAAAAAATACTGTGAATGTTTTCAGgtttcaactc ... cttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCTTTTGGAAAACGGGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttttttcttcttaatccctctgtatgcatcttatctttactcttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCTTTTGGAAAACGGGAGG
            tcttaat  putative branch site (score: 125)
                                tcttatctttactctt  putative PPT
     tttttcttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcaactcctacattgatttaatgctctctcttttttcttcttaatccctctgtatgcatcttatctttactcttcatcaagGGTGGTGTGGGATGCTCCATAAGTTGCAGATGCGAGGGCTGTAAGAATGCTTTTGGAAAACGGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG