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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgtatgcctttactaatgcctattttttcagaggtgcactgactttaccttggcacaaattctttctcgcacctctaagtaattagctatggttctgaaaattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAATTGGAGCATCAGCACCAATTT

Basic information

species Zea mays
transcript GRMZM2G068277_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068277_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 7
gtatgtttgtatgcctttactaatgcct--attttttcagag---gtgcactgactttaccttggcacaaattctttctcgcacctctaagtaattagctatgg-ttctgaaaattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAATTGGAGCATCAGCACCAATTT
||| || ||||    || | | ||  ||  |  |   || ||   ||   || ||||||   | | | |||||||   |   | |       | |||   |||| | |||||| ||| ||| ||| ||||||||||||||||||| ||||||||||| |||||||||||||||||||| |||||||| |||| |
gtacgtgtgtagatattaagtgattgctcaaactccacatagccagttagctcactttattctagtagaaattctggattatatcc------acttactgatggctcctgaaatttcaaaagGTCCTGGAGCAAATTCTTGCTGTACTTATACAGTTCGTTAAAGACAAGAAATTGGAACATCAGCATCAATAT
















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|71428336|gb|DR809386.1|DR809386
EST:     TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
EST: gi|71443221|gb|DR824271.1|DR824271
EST:     TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
EST: gi|5895704|gb|AW036950.1|AW036950
EST:     TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
EST: gi|110488821|gb|EE012728.1|EE012728
EST:     GAACATTATAAT                         GTCTTGGAGCAAATTCTTTCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: GAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
EST: gi|45568053|gb|CK985878.1|CK985878
EST:     ATGGACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: ATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
EST: gi|60337416|gb|DN204389.1|DN204389
EST:     TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTC
genomic: TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTC
EST: gi|148948940|gb|EC894359.2|EC894359
EST:     GACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: GACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
EST: gi|110504829|gb|EE017437.1|EE017437
EST:     ATGGACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTTATACAGTTTGTTAAAGACAAGAA
genomic: ATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGC-TTATACAGTTTGTTAAAGACAAGAA
EST: gi|60347346|gb|DN214319.1|DN214319
EST:     TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: TCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
EST: gi|50324448|gb|CO519574.1|CO519574
EST:     CCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: CCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
EST: gi|74237081|gb|DT644995.1|DT644995
EST:     AAATTTGCTGAACATTATAAT                         GTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA
genomic: AAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAA

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: 240

GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAATTGGAGCATCAGCACCAATTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 125

GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAATTGGAGCATCAGCACCAATTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 105

GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAATTGGAGCATCAGCACCAATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

GGTAAAATTAATCATCGAAGAGATAGAGAAGGAAGAGGCACATCTCCTGGAGGACCTTGCTTCAATGGACAGAAAATTTGCTGAACATTATAATgtatgtttgt ... aattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAATTGGAGCATCAGCACCAATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaattctttctcgcacctctaagtaattagctatggttctgaaaattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAATTGGAGCATCAGCACCAATTT
                     taagtaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttgtatgcctttactaatgcctattttttcagaggtgcactgactttaccttggcacaaattctttctcgcacctctaagtaattagctatggttctgaaaattccaaaaGTCTTGGAGCAAATTCTTGCTGTGCTTATACAGTTTGTTAAAGACAAGAAATTGGAGCATCAGCACCAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA