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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttcttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 28
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 45
gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttcttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG
                                      |   ||    |      |  |    |     | | |||   || || | |    || |  |  ||||||||||| | || ||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||| |||||||| || |||||||| || ||||||||
-------------------------------------gtatgtggttatttgctagctatggatgtgcatgtatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 28
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 47
gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttctt-ctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG
     ||       ||    |  |  || |  |||    || ||| ||    | |       ||   ||| | | |  ||||    ||| |  |  |||  | ||| |||||||||||||| || || ||||| |||||||||||||| || ||||| ||||||||| | ||  | |||||  |||||||||| |||||  |||||||
---attgtcaagaagcagagttgaaattgccaaattctatcttgatatgttttgt----tcattaaaattttgttcagtatt---aacatttatttttttgtgcttgcagGTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 28
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 48
gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttcttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG
     ||       ||    |     || |  |||    || ||| ||    | | |  | ||    ||| | | |  ||||    |||    |   ||  |  | |||||||||||||| || || ||||| |||||||||||||| || ||||| ||||||||| | ||  | |||||  |||||||||| |||||  |||||||
--ctttgtcaagaagcagagttagaattgccaaattctctcttgatat---gttttattcattaaa-attttgttcagtatt---aacatgtatttgtttgtgctgcagGTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 28
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 47
---------------------------------------------gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttcttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG
                                             |||||    |  | |  |  ||       ||     |    |     |   |||  |   |     | ||   ||   ||| ||||| | | |   | || |  || || | || || || || |||||||||||||| |||||| || |||||||||| |||||| | ||| | ||||| |||||||||||||| ||||| || ||
gtattttaggacaatcattgttcacataactcaagtagttgttacgtacagccctact-gtctattatgcaacacttgcctttcctacttgctacaatcacagtgtcaaattgtttagtattgtatatctgataattgct-tgtccttgttaagCTCCTCCAAAGCACCATATATGAAGTTGATCTTGATAGACTTCTTCAGAGTATCCATGTATATCTGCAAGATCTGGGAATGGAAGAGATACGTAGGAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 28
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 17
gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttcttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG
            ||| ||||   ||| ||  |||  |    ||| ||||   |  |       | || | || |   | || ||  | |   |      | |  | ||||||||||| ||||| |||| ||| ||||||||||| || || ||||| || || ||| | ||  | |||||| ||||||||||||||||  | |||||
-------tcaacttgtttgaattatggtt--gaacattaatatgtcattctcttggtatgggcttctgtgctatgatcaatctcatagatcagcttccacatggtgcagGTTCTTCAAAGTACTATATTTGATGTTGACCTTGACCGCATCCTTCAAAGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 28
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 3'ss of exon 46
gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttcttcttt--cagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG
||     | || ||   | |||  | | |   |||   ||  ||    |   ||||||   |||  || |   |  |   ||  | ||    | |  |  || | |  |||||||||      ||  |   |||||| |||||||||||||||||||| ||||| ||    |||||  |||| |||||||||| ||||||||||| | |
gtttggaactgattttctcatat-tctcttgaaattgatttgtgtttctttttctgac---ttttgtactacgtgtgg-gttgttaacgtgtgaagctgtttttatggcagGTTCTTGGTTCAACTTTGCTTGAAGTAGACCTTGATCGAATTCTTCAAAGCATTCACGAGTATTTTGAAGAGCTGGGAATGGCAGAAATACGGAAACG

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|18450668|gb|BM428946.1|BM428946
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGCCAAAG                         GTTCTTCAGAGTNCAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
EST: gi|194717113|gb|FK934266.1|FK934266
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACGAAG                         GTTCTTCAGAGTAC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTAC
EST: gi|61118500|gb|DN559461.1|DN559461
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTCTTCAGAGTACAATATATGAAGTTGACCTTG
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTG
EST: gi|87152573|gb|DY397362.1|DY397362
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
EST: gi|32847226|gb|CD986907.1|CD986907
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTCTTCAGAGTA
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTA
EST: gi|67035401|gb|CO463934.1|CO463934
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCANATGTTTAATTAAGTTGACAAAG                         GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
EST: gi|22489973|gb|BU049896.1|BU049896
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
EST: gi|19822797|gb|BQ048821.1|BQ048821
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTCTTCAGAGTNCAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
EST: gi|19822549|gb|BQ048573.1|BQ048573
EST:     ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC
genomic: ATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGC

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: 215

CCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTGCTGTAAAAAATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 21

CCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTGCTGTAAAAAATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

CCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTGCTGTAAAAAATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

CCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTGCTGTAAAAAATCAGAAGTTTTCAGACTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtacatgatt ... cttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacacttttcctattctctacgctatttctgacactcgtaatttcttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG
                           ttctgac  putative branch site (score: 80)
                                       taatttcttctttc  putative PPT
                                       taatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttcttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA