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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG

Basic information

species Zea mays
transcript GRMZM2G150098_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
--tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
   |     |   |   || |   ||| ||  |      | |||    |  ||||  ||    ||  ||| ||||| ||  | |  |  | ||  | |  ||||||| ||||||||||||||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||||||||| ||||||||||||||||| |
ttcgtgatgatgataatacatatgagg-tgcctggtaatttaccatgctg-gttatgttgctgtgcgtctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG

upper sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
--tgacgctacatt--tccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
    |  |||  ||  ||    |  |||    | || || ||        ||| | || |||| |     |||||||   || |   ||| || |    || |||||||||| || || || ||  | || ||||| || ||| || | ||||||||||| || ||||| ||  |||||||||| ||||||||||| ||||| |
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaa-ttcaga-aatcctgattt--atatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG

upper sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
-tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
 |    | | |||| |||   ||| |  | ||   |  ||     |||  | ||        |  |||||| | | ||  |  |  ||||    | || ||||||||||||| || |||||  | |||||||||||||||||| | || || ||||| || ||||||||  | |||||||| || |||||||||||  | |
gtacttcaaaattttcac---gtatggcgattgcattttatgtatattgaggta--------taaatctgact-cttttctctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG

upper sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
           | | |  |   |   | ||| |||  |  |  ||    |||   || | |  | |  ||||   | | |   ||  || |  |||  |||||||||||||||| || ||  | || || |||||||| ||| | || |||||||| || ||||||||| | |||||||| || |||||||||||  | |
----------gtacaaagttacaccttatttcacttgtggctaaa----gttggttttaaa--ggtaggattg--tgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG

upper sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
tgacgctacatttcca--cctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
  | |  | ||| |      |    || | ||  |    |        | | ||     |  |  ||| || |||  |   || |  | |     | | |||||||||||||||||||||||| | ||||| ||||| || ||  | ||||||||  | || ||||||||  |||||||||| ||||||||||| ||||| |
--atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG

upper sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatc--tgatttccttaatgatatggttctgcta--tgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
    |||   ||      |||| |     ||| ||   |      ||   | ||  |  ||| |     ||   || |   |  | ||| | |  |   || |||| |||||||| ||||||||| | ||||||||||| ||  || | ||||| ||| | |||||||||||  | |||||||| ||||||||||| ||||| |
----gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG

upper sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S90_133V6.1 (Physcomitrella patens), 3'ss of exon 3
--tgacgctacatttccacctggtaggct-gttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgct--atgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
  |   ||   |  ||     |      | | |  | | |  || |||      || |  |||||   | || | |   |  || | ||  || | |  ||||||||||||||||| || ||| | || ||||| || || || ||||| ||| | ||||   | ||||| ||||||||||| ||||| ||||||||||||   |
cttattgcggaagatcttatcgaagccttagctgcatttcacactgaa----aatatcaacacatccgtttgttgtgggtgttg-tttgaatcggatcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG

upper sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S392_18V6.3 (Physcomitrella patens), 3'ss of exon 3
tgacgctacatttccacctggtaggctgttttactcctaac-cgaattctgttaacttcacatggatctgatttc---cttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
   |  |||| |   |  | | || |  || |     |  | ||  || |  | |||   ||  |  ||  | ||     | || || || |    | ||||||||||||||||| || ||| | || || || ||||| || ||||  ||||| ||||   | |||||||| ||||||||  ||||||||||||||||    |
-ttcattacaat---aatttggagacgattctctctgtgtctcgtcttttcgtgactctgcaatgcgcttgtctcgcttctcatcatttgatggatccatgcagGTTGAGAACCAGGAAGGTCTGGTCAATTTCGATGACATTTTGAAAGAGACGGATGGAGTGATGGTTGCAAGAGGTGACTTGGGAATGGAGATTCCGACTG

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|78112798|gb|DV531192.1|DV531192
EST:     TCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAGGTTGATGTCAAAG                         GGTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGG
genomic: TCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAGgttcgtatat ... tgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGG
EST: gi|31353381|gb|CD437738.1|CD437738
EST:     TCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAACTTGATGTCAAAG                         GTTGAAAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACT
genomic: TCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAGgttcgtatat ... tgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACT
EST: gi|71444667|gb|DR825717.1|DR825717
EST:     CAGACAGGTTCTTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAG                         GGTGAGAACCAAGAGGGTGGTGTAAACTT
genomic: CAGACAGGTTCTT-GGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAGgttcgtatat ... tgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTT
EST: gi|71428007|gb|DR809057.1|DR809057
EST:     TCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAG                         GTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACT
genomic: TCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAGgttcgtatat ... tgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACT

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: 83

TGACATGATTGCTCTATCCTTTGTCCGTAAAGGATCAGATTTGGTGACTGTCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAGgttcgtatat ... tgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 134

TGACATGATTGCTCTATCCTTTGTCCGTAAAGGATCAGATTTGGTGACTGTCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAGgttcgtatat ... tgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TGACATGATTGCTCTATCCTTTGTCCGTAAAGGATCAGATTTGGTGACTGTCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAGgttcgtatat ... tgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 52

TGACATGATTGCTCTATCCTTTGTCCGTAAAGGATCAGATTTGGTGACTGTCAGACAGGTTCTTGGGCAGCATGCCAAGCGCATTAAGTTGATGTCAAAGgttcgtatat ... tgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
                                          ttctgct  CT-rich tract
                              ttaatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - gctacat
- - - - - - - cacctgg
- - - - - - - - - - - -ggctgtt
- - - - - - - - - - - - - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatgg