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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG

Basic information

species Zea mays
transcript GRMZM2G126594_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G37160.1 (Glycine max), 3'ss of exon 5
gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttctt-catttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
||| |||   || | |   |||||  || | | |    ||| |||  | || |||       || | |    |  | | |   |  | ||||||||||||| || ||||||||||| ||||| || ||||| ||||||||||| || ||||||||||||
gtatgtc--actgatttt-gttgatattgt-cgacttaatggactactattacatgcttttgttgaga----gagtcctttttttttgcagCTTACATGTCATCTCCATGCCACATTGAGCTGATATTGTCTGAGAAGGAAGAGCCTGTGAAGAAAGAG

upper sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G01110.1 (Glycine max), 3'ss of exon 5
gtaagtctatctaactaaagttgaagtt-ttgct-atgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
       ||| |  ||    |||  | | |  || |    ||| | |  | ||  ||     ||||   ||  |  || ||   |  | ||||||||||||| || ||||||||||| ||||| || || || ||||||||||| || |||||||| |||
------gtatgtcgctggttttgttgctatcactgacttaatggattactattactt----actta-tgttgagagtgtcttttttttgcagCTTACATGTCATCTCCATGCCACATTGAGCTGATATTATCTGAGAAGGAAGAGCCGGTGAAGAAGGAG

upper sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctgg--tccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
                    ||| |  |    ||       | || ||  | ||     |  | ||  || ||||| ||  || |  | ||||||||||||||  |||||||||||| ||| | || ||||| ||||||||||| || || || ||||||
-------------------tttgtaaatcacttacattgatagctttttgtaatccattgtatgac--tcagtttgtctttcttggttgcagcttacatgtccaacccatgccacattgagTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG

upper sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G67430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctgg--tccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
|||||| |         |  ||| |  |    ||       | || ||  | ||     |  | ||  || ||||| ||  || |  | ||||||||||||||  |||||||||||| ||| | || ||||| ||||||||||| || || || ||||||
gtaagtttga------gattttgtaaatcacttacattgatagctttttgtaatccattgtatgac--tcagtttgtctttcttggttgcagCTTACATGTCCAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAGGAAGAGCCTGTCAAAAAAGAG

upper sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagcttaacattctgtttg--cctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
||| ||||   |  |||         |||| | | |   ||     |  ||||  | | |||  ||  ||  |||    ||| ||  | |||||||||||||   |||||||||||| ||| | || ||||| ||||| ||||| || ||||||||||||
gtatgtcttcttttctattcgactgtttttacaacgtt-tgtttcttcattcacattgtgct-gactctcgatttaattctatcttatgcagCTTACATGTCAAACCCATGCCACATTGAGTTGATTTTGTCAGAGAAAGAAGAGCCTGTGAAGAAAGAG

upper sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S97_78V6.3 (Physcomitrella patens), 3'ss of exon 3
--------gtaagtctatctaactaaagttgaagtttt--gctatgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG--------------------------------
            |  ||| | |  || |||  ||||||  | |  | |   | |  |   ||| |   |     |||||   | ||    |    | |||||||||||||||| || |||||||| ||||||||  | || |||||||| |  |||||   ||||| |                                
gtgctatttcccgattattttataaatgttttagttttatgttcagtgggaacccctgtgtcactaacaatgatacattgcctctgatgtcgatttgcagCTTACATGTCCTCTCCCTGCCACATTGAGCTCATTCTTTCTGAGAAGGAGGCGCCAGTTGCGAAAGCGGTAGAGGTTTCTGAACCCAAGACGCGCAGGAA

upper sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S38_376V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------gtaagtctatctaactaaagttgaagttttgctatgcg-atgaactgttcttcatttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
                                |||| ||  | |       ||  ||  ||||  | |    ||||       |  |    |  | |   |  ||      |   || | |||||||||||||||| || |||||||| ||||| ||| | || ||||||||||  |||||||||||||||
gtaagtggctactccattcctactgttgtgttgtaattcgttatggaacctgtgtaatgtttggcacgtacgtgaatcccgtgttgtcacaaattgatggtgttgcccat-tgggtgttgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTGATCCTTTCTGAGAAGGAAGCGCCAGTGAAGAAAGAG

upper sequence: GRMZM2G126594_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S364_56V6.2 (Physcomitrella patens), 3'ss of exon 3
------------gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
             | || |  |    ||  |||| |   |   || ||      |||   | | ||    |    |||       || | | | |  | |||||||||||||||| || |||||||| |||||| || | || |||||||| |  ||||| |||||||||
tgcactcttgaactgagccc-ttacccttgagttaacaatggcctctgaatgtgacttcacctaatcataattacaactaataacttacgt-cgttatgcagCTTACATGTCCTCTCCTTGCCACATTGAGCTCGTCCTCTCAGAGAAGGAGGCTCCAGTAAAGAAAGAG

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|211085646|gb|FL305426.1|FL305426
EST:     GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACC                         CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
EST: gi|166666607|gb|EG180228.1|EG180228
EST:     GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACC                         CTTACATGTCCTCCCCATGCCAC
genomic: GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCAC
EST: gi|4647043|gb|AI622118.1|AI622118
EST:     GGCTCAGAAGCAGCGACGCAGGACATNCCGTGCTCATGGACGCATCAACC                         CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
EST: gi|71301596|gb|DR786860.1|DR786860
EST:     GGCTCAGAAGCAGCGACGCAGGACATCCCGTGTTCATGGACGCATCAACC                         CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
EST: gi|71301597|gb|DR786861.1|DR786861
EST:     GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACC                         CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
EST: gi|14997333|gb|BI319308.1|BI319308
EST:     GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACC                         CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
EST: gi|50333910|gb|CO529036.1|CO529036
EST:     GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACC                         CTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG
genomic: GGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 489

AAAGGACTTGATGTGGATACCCTCTATGTGTCGCACATTCAAGTTAATCAGGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 360

AAAGGACTTGATGTGGATACCCTCTATGTGTCGCACATTCAAGTTAATCAGGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 418

AAAGGACTTGATGTGGATACCCTCTATGTGTCGCACATTCAAGTTAATCAGGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

AAAGGACTTGATGTGGATACCCTCTATGTGTCGCACATTCAAGTTAATCAGGCTCAGAAGCAGCGACGCAGGACATACCGTGCTCATGGACGCATCAACCgtaagtctat ... cctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgatgaactgttcttcatttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG
                        gcttaac  putative branch site (score: 229)
                                         cctacct  putative PPT
                          ttaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctatctaactaaagttgaagttttgctatgcgatgaactgttcttcatttggagcttaacattctgtttgcctacctggtccagCTTACATGTCCTCCCCATGCCACATAGAGCTCATCTTGTCGGAGAAGGAAGAACCAGTGAAGAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA