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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccatacatcgattgtacttcacgtttgcagccttgatattgagctgatctctactcttgaatgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT

Basic information

species Zea mays
transcript GRMZM2G074169_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074169_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g37420.2 (Oryza sativa), 3'ss of exon 3
-----------------------------------gtaagccatacatcgattgtacttcacgtttgcagccttgatattga-gctgatctctactcttgaatgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT
                                     || |      || |   || |  ||  ||||   ||  ||||  | ||||| | || ||||  |||| |   ||| ||||| || ||   |||||||||||| |||||||||||||| || |||||||| |||||||||||||| | ||| ||| |||| ||||||||||| ||
gtgagatatattttctttcatttcataattaatgatgaaactgactgtcaacattattaaaccattgccatctcaatatcaaagctgacccctcctctccaatgcacgtagGCAAAGACGCAACCAATGATTTTGAAGACATTGGCCACAGTGAATCAGCAAGGGAGATGATGGAGAAGTATCTCATTGGGGAGATTGATGCTTCAACCAT

upper sequence: GRMZM2G074169_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G41010.3 (Glycine max), 3'ss of exon 3
------gtaagccatacatcgattgtacttcacgtttgcagccttgat--attgagctgatctctactcttgaa-tgtaac---cagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT
       ||   |||     |||| |  || |      ||     |           |||| | |  || ||   |||      ||||||||||||| ||   ||||||||||||| |||| ||||||||||| || || || |||||||| || ||| |||| ||  |||| ||| | |||||  |
gtatgcttatatcatctgaagattattattaataaaaacactaaagggtagccatattgatatttgatcatgctctgtggattacagGGAAAGATGCAACCAATGATTTTGAAGATGTTGGACACAGTGATTCTGCTAGAGATATGATGGAAAAATACTACATTGGTGAGATTGATTCATCAACTGT

upper sequence: GRMZM2G074169_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT5G53560.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtaagccatacatcgat-tgtacttcacg-----tttgcagc--cttgatattgagctgatctctactcttgaatgtaac---cagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT
   |||  | |   |   | | |  |||| |     |||| |||  || | |       |    |||  | | |  | |      |||||||||||||||||  ||||||||||||  |||| ||||| ||  | ||||||||||||||||| || ||   ||| ||  |||| ||| | || |   |
gtataaaacttgtgtttctctctgattcaaggcggatttgaagcggctcggtgactgtttctgttctgatgtggtgttttgtttgcagGGAAAGATGCTACAAATGATTTTGAAGACGTTGGTCACAGCGACACTGCAAGGGACATGATGGACAAATATTTCATTGGTGAGATTGATTCGTCTAGTGT

upper sequence: GRMZM2G074169_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0098g01230.t01 (Vitis vinifera), 3'ss of exon 3
gtaagc---catacatcgattgtacttcacgtttgcagcct--tga-tattgagctgatctctactcttg-----aatgtaac--------------cagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT
|||||    |||| |||   | ||   ||   |  || |||  ||  ||   | | |||   | | | |      || || ||              ||||||| ||||| |||  ||||||||||||| | |||||||||||| | || || ||||||||||| || ||| |||| ||  |||| ||| | ||||   |
gtaagttatcatatatcacctctagc-caatctcacaccctgttgtctaccaaaccgattagtgcccctacacacaaagtgactgaattttcttctgcagGGAAGGATGCGACAAATGATTTTGAAGATGTAGGCCACAGTGATGCAGCCAGAGACATGATGGAAAAATACTACATTGGTGAGATCGATCCCTCAAGCGT

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|32937079|gb|CF041898.1|CF041898
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211368304|gb|FL143997.1|FL143997
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211153264|gb|FL390947.1|FL390947
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211520264|gb|FL466401.1|FL466401
EST:     AGGTTTTGCTAGCTGTACCTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: AGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211220054|gb|FL422612.1|FL422612
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211368306|gb|FL143999.1|FL143999
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211385748|gb|FL435722.1|FL435722
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211368307|gb|FL144000.1|FL144000
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211103116|gb|FL195450.1|FL195450
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTG
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTG
EST: gi|211467880|gb|FL454208.1|FL454208
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
EST: gi|211368305|gb|FL143998.1|FL143998
EST:     TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG                         GGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA
genomic: TTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAA

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: 394

GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1128

GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 859

GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 597

GTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTGgtaagccata ... atgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcacgtttgcagccttgatattgagctgatctctactcttgaatgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT
                          agctgat  putative branch site (score: 597)
                 ttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccatacatcgattgtacttcacgtttgcagccttgatattgagctgatctctactcttgaatgtaaccagGGAAAGATGCTACAGCTGATTTTGAAGATATTGGCCACAGTGATTCCGCAAGGGACATGATGGAGAAGTACCACATCGGGCAGATAGATGCTTCAACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT