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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttattgtgccttggtttgattttgcatgtacaagtacagaggatctgagttaccaaggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA

Basic information

species Zea mays
transcript GRMZM2G179308_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
gtatgttattgtgc------cttggtttg-attttgcatgtacaagtacagaggatctgagttaccaaggtt-ctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA
||||||| ||| |        |||||||| ||| |      ||||   |||    | |||||||| || | | | |||||| || ||  | || ||||| || ||||||||||| ||||| |||||||||||||||||  |||| ||||||||||  || ||| |||| ||||||||
gtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 8
----------------gtatgttatt---gtgccttggtttgattttgcatgtacaagtacagaggatctgagttaccaaggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA
                | ||  | ||   |    ||  |    |||||  |||  || |    ||  | || | | | |      |||||||||| ||  | || |||||||| ||||| || || ||||||||||||||||||||||| ||||| ||| | ||| | || ||||| ||||| |  ||
gtaagtttggctctctggatactttttaggcaattttatccagttttgtttgtttaaatc---agcttatgggcttcta-----ttgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCTATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
--------------gtatgttattgtgccttggtttgattt-tgcatgtacaagtacagaggatctgagttaccaag--gttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA
               |    |  |||           |||| | ||| |   ||     |     | | ||   ||    |  | ||||| |  ||  | || |||||||||||||| ||||| ||||| || |||||||| ||||| ||||| || || ||| | |  ||||| ||||| |  ||
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
----gtatgttattgtgccttggtttgattttg-catgtacaagtacagaggatctgagttacc----aaggttct---gcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA
    || ||    | ||  |   |||||  ||   ||   | |||        | | | | | |     || ||||   ||||||||| ||  | || |||||||| ||||| || || |||||||| |||||||||||||| ||||| ||| | ||| | || ||||| ||||| |  ||
gtaagtttggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 8
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------gtatgttattgtgccttggtttgattttgcatgtacaagtacag-----aggatctgagttaccaaggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA
                         ||||  || |   | |     |     | |||| |  | ||        |  | ||   ||       |  |  ||||||| ||| | || |||||||| || |||||||| ||| |||||||||||||| ||||| | || ||  | ||    || ||| | | |||||||||
tccctcgaagaaggctactgtagctgtat-ctactacacatgacggtagccgtacatggatcaatatgtcttttaataactttattcattgtttgttttagGGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGA

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|32787565|gb|CD936467.1|CD936467
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|45568628|gb|CK986157.1|CK986157
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|76015336|gb|DT942506.1|DT942506
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|71756384|gb|DR954321.1|DR954321
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|76015337|gb|DT942507.1|DT942507
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|211429794|gb|FL437778.1|FL437778
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|211241890|gb|FL451479.1|FL451479
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|60357877|gb|DN224850.1|DN224850
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|33096467|gb|CF056461.1|CF056461
EST:     GTGATATCTGGAGTGTTGGTGGTATTCTTGTTGAGC-TTGNCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGAT
genomic: GTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTG-CACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGAT
EST: gi|60347445|gb|DN214418.1|DN214418
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG

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), 27 (downstream exon)
Score: 321

GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 231

GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 265

GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA


Block sizes: 49 (upstream exon), 27 (downstream exon)
Score: 337

GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttatt ... ggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttgattttgcatgtacaagtacagaggatctgagttaccaaggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA
  gtttgat  putative branch site (score: 337)
     tgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttattgtgccttggtttgattttgcatgtacaagtacagaggatctgagttaccaaggttctgcagGGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG