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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat...

Basic information

species Zea mays
transcript GRMZM2G114793_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacgacaatgaaatacttctgat-tattgtactattatcttattaccagatgcttat-----
|||||||||||||||||||| || || |||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||    |||   |||    ||   ||| ||    ||   || |  |  |  || |   | | | ||  ||||| |  | | |||    |||  | ||     
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgctttt--atttgccct---taggtactaaatat-ctgcttctgtacaacatcacagttgtagagtactgtagtttgattcaatgattttcatgcaac

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacg-acaatgaaatacttctgatt-------attgtactattatcttattaccagatgcttat---------------
|| ||||||||||| ||||| || |||||||| ||||||||||| ||||| || ||||| |||||||| || || || ||||| || ||||||||||||||| |||   ||||    |||  | | |  |        |   | || | | ||  | ||| |  |  ||       ||| | || | || ||| | |  | |   | |               
GTTTTTGACCTTGGGGGTGGAACATTTGATGTTAGTATCTTGACAATTGATAATGGTGTTTTTGAGGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagaattttttttttttatgagtcttaataagaagaacttattatgtagaaaaatatattattctttccaccaaattctcctctgatgttaatgcttgctatgtctccttcgccttgccag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaatttt--cccattaaaactatctagctatcccatgcactacgacaatgaaat---acttctgattattgtactattatcttattaccagatgcttat---------------------
|||||||| ||||||||||| || |||||||||||||||||||| ||||| || ||||| ||||| || || ||||| ||||| || ||||||||||||||| ||    |||   | |||  | || | |||  | ||   |   ||| |  ||||||||   |       |  ||  | | ||   ||  |  |  |||  |                       
GTCTTTGATCTTGGTGGTGGGACCTTTGATGTCAGTATCTTGACAATTGATAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGgtgagtacttttatacacatacacacaagctaa-tgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaa----aactatctagctatcccatgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat---------------
|| ||||||||||| ||||| || |||||||||||||||||||| ||||| || ||||| |||||||| || || || ||||| || ||||||||||||||| |||   ||||   || |     ||  |   |    |   ||| |  |  |  || |     | |  |  ||| |  | | || ||| | |  | |  || |               
GTTTTTGACCTTGGGGGTGGAACATTTGATGTCAGTATCTTGACAATTGATAATGGTGTTTTTGAGGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccat-------taaaactatctagctatcccatgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat-----
|||||||| ||||||||||| || |||||||||||||||||||| ||||| |||||||| ||||| || || || || ||||| || ||||||||||||||| ||    |||   ||         || |  ||  |   |    ||  | |    | || ||||  |  |  | ||  || | |  |  |||| |    | |   |     
GTCTTTGATCTTGGTGGTGGGACCTTTGATGTCAGTATCTTGACAATTGATAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagtacttttatacacatacacacaagagaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtc-tgctatttctgtttccccttactag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttc-ccattaa--aactatct--agctatcccatgcactacgacaatgaaatact-tctgattattgtactattatcttattaccagatgcttat----------------------------------------------------------------
|| ||||| ||||||||||||||||||||||||||| ||||||||||||| ||||| ||||||||||| ||  |||| ||||||||||||||  | |||||||| | | || |  |||  ||  || | | |  |  |      ||  | |  ||||   | | || |   | |    ||   | | | || |     |    | |                                                                
GTGTTTGATCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaatatacttgtgaccaggaatgaattgttttgaattgcattgtgttcaataacaaatgattgctatgccaatgcaataagctaaacatagtcaataacatgtgtcagaatggagggattgttttagtgtgatgttggtggtaaccttttgttgttatgatctgcgcag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat---------
|| ||||||||||||||||||||||||||||||||| ||||||||||||| ||||| ||||||||||| ||  |||| ||||||||||||||  | |||||||| | |   ||   |  |  | |   | | | |    |||| || |  |||||| |  ||||||  |||| | | |    | | || || ||| ||           
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaata--cttgtgaccacgaatgaattgttctgaattgcattaag--aatgaattg-ttctga--attgcattgtg--ttcaataacaaatgattgctgtgccaat

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcc--catgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat
|| ||||| |||||||||||||| |||||||||||||||||||| || ||||| ||||| |||||||| || ||||| ||||| ||||||||||| |||||||||  | |  | || |     ||| ||   | |    |||    | |        | || ||  | ||   | | | ||    | ||   |||  | | |
GTGTTTGATCTTGGTGGTGGTACATTTGATGTCAGTATCTTGACAATCGACAATGGTGTTTTTGAGGTTCTTGCCACTAATGGAGACACTCATCTGGGAGgtaagc-attgcttccttggtccctaccttatttttgtgcattttttcctttgtaagattagttacggtttaaggattcttggtgtgttgt-agagacctct

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacg-acaatgaaatacttctgattattgtactattatcttattaccagatgcttat--------------------
|| ||||||||||||||||| || || |||||||| |||||||| |||||||| ||||| || ||||| || || || ||||| ||||||||| | |||||| || || ||||  |  ||    |        |||   ||| ||  | ||| ||||| |    | |  |  | |   ||||  || |    |||||| |                     
GTTTTTGACCTTGGTGGTGGAACCTTCGATGTCAGCATCTTGACTATTGACAATGGTGTTTTCGAGGTTCTTGCTACAAATGGAGACACTCATTTGGGAGgtgag-gatttttttctctactgatgctctttcatctt-tgctctttgcacattgaaagaaaatttacgagaggaaagttattatactgt-ggatgctcaaggttcaattctttcctgcag

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat
|| ||||| || |||||||||||||| ||||||||||||||||| || |||||||| |||||||| ||| || | ||||| || ||||| |||||||||||||         |   || ||| |  |||   | ||      ||  |   ||    | |  |   | |   |                            
GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgta--------ctttgatcaaagccttctccttttctttcttacagctcgaaactgacatctaccaatgcag----------------------------

upper sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 4
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat
|| ||||| || |||||||||||||| ||||||||||||||||| || |||||||| |||||||| ||| || | ||||| || ||||| |||||||||||||         |   || ||| |  |||   | ||      ||  |   ||   || |  |   | |   |                            
GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgta--------ctttgatcaaagccttctccttttctttcttacagctcgaaactaacatctaccaatgcag----------------------------

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|32837915|gb|CD977593.1|CD977593
EST:     CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGGATCATGGAGT
genomic: CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGT
EST: gi|17970215|gb|BM276979.1|BM276979
EST:     CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|32941599|gb|CF046418.1|CF046418
EST:     CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGGATCATGGAGTAC
genomic: CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTAC
EST: gi|67028334|gb|CO457083.1|CO457083
EST:     CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|67029818|gb|CO458567.1|CO458567
EST:     CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGA
EST: gi|211320984|gb|FL255014.1|FL255014
EST:     TGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGAGTCAAG
genomic: TGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGA-TCAAG
EST: gi|7135132|gb|AW497932.1|AW497932
EST:     CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAG                         GTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGA
genomic: CAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGA

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), 47 (downstream exon)
Score: 268

GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 279

GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 210

GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 920

GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaat ... cctcattcagGTGAGGACTTTGACCAGAGGATCATGGAGTACTTCATCAAGTTGATCAAGAAGAAGTACAGCAAGGACATCAGCAAGGACAACCGTGCTCTTGGAAAGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG