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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcccggtcacagacacacttgctcagttttctggaagctctgactttaaatattttagtgtgtggtatttggattcagtgagtttcactattccctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT

Basic information

species Zea mays
transcript GRMZM2G402242_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------gtctcccggtcacagacacacttgct-cagttttctggaagctctgactttaaatattttagtgtgtggtatttggattcagtgagtttcactattc-cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT
                                                    | ||     |    |    | ||  | |||   | |  || | |  ||||| |  |||| | ||  |   ||| |   |||||   |   || |    | |  ||||||| ||||||||| |||| || ||||||||||| ||  | |||||||||||||||||||||||||| ||||||||||| |||||||| || ||||| || |
gttcccctcccctctgccaccaacacaacaacacctgtctgctgcagcttttgccttttaatattggttctattttttacagacattt--aatcaccaacttttaccatttaaatgcat---attcg---tcagttgctgatacaaccgacttattgcagTATGGCCTGCCATTGAAAATAGTTTCCTATAAGGACCTCTATGGCTGGACAATGGATGATATTGTGAAAGCAATTGGCCTAAAAAATAACTGTACCTTTT

upper sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------gtctcccggtcacagacacacttgctcagttttctggaagctctgactttaaatattttagtgtgtggtatttggattcagtgagtttcactattccc----tgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT
                                           |   |    ||      | | | | ||  |||| |  |     | | |    |  |||||   | |   ||    ||||      |     ||   ||    |  ||||||| ||||||||| |||| ||  |||| ||||| ||  | |||||||||||||||||||||||||| ||||||||||| |||||||| |||||||| || |
gttcccctcccctctgccatcaacacaataatgcctgtctgctgcagctttttccttttaatattggttctattttttacagatatttaatcaccaacttttaccatttaa-atgcatattcgtcagttgctgatacaaccgacttattgcagTATGGCCTGCCATTGAAAATAATTTCTTATAAGGACCTCTATGGCTGGACAATGGATGATATTGTGAAAGCAATTGGCCTAAAAAATAATTGTACCTTTT

upper sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 3
gtctcccggtcacagacacacttgctcagttttctggaagctctgactttaaatattttagtgtgtggtatttggattcagtgagtttcactattccctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT
             |  |   |||  | | || | ||   | |  |    | | | ||||| || | ||| ||| | ||   || |||      ||  ||  | ||||| ||  |||| || ||||||||||| ||||||||| ||||||| |||||||||||||| ||||| |||   |||||| | || |||||||| || || |
-----------gtaagc-ttctttttgaattctatgtgtgttaag----tgattgtttta-tg-gcggtttttag-tttgatgggttctttatttttctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACAATGGATGAGATTGTGAAAATGATTGGTTTGAAGAACAATTGCACCTTTT

upper sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G76170.1 (Arabidopsis thaliana), 3'ss of exon 3
gtctcccggtcacagacacacttgctcagttttctggaagctct-gactttaaatattttagtgtgtggtatttggattcagtga-gtttcactattccctgctg---cagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT
                                   | ||||| | || ||||  | || | |||| |     |   |||  |||| | ||    ||||  || |    ||||| ||  |||| ||  |||||||||| || |||||| ||||||| ||||||||||| || ||||| ||    || ||| | || |||||||| || ||||
-----------------------------------gtaagcttttgaatttatgtgttat-gtgt-tcactctaaaattttgtgatgatttgtcattctttgttttcccagTATGGATTGCCTCTTCAGATTGTTTCATACAAAGATCTGTATGGATGGACAATGGACGAGATTGTGAAGATGATCGGTTTGAAGAACAATTGCACCTTCT

upper sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 3
-gtctcccggtcacagacacacttgctcagttttctggaagctctgactttaaatattttagtgtgtggtatttggattcagtgagtttcactattccctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT
  ||| |         |      |  |          |||| | |  |||||  | || ||     |  ||| ||  ||   |   |||   | ||   | |  ||||| ||||||||||||||| |||| || || || ||||||||||| ||||| |||||||| || || ||    || ||| |||| ||||| || || || |
aatcttctaaatgtctatgagtatatttcaaag--cagaagatgtttcttta--ttttctaaataatattatctgttttttct---tttttgtttttttttcctcagTATGGCCTGCCACTGAAGGTTGTATCTTACAAGGATTTGTATGGATGGACGATGGATGAAATAGTGAAGATGATAGGTTTAAAGAACAACTGCACATTTT

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|74232164|gb|DT640078.1|DT640078
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|71774415|gb|DR972293.1|DR972293
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|37419554|gb|CF647460.1|CF647460
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGAT
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGAT
EST: gi|37416521|gb|CF645910.1|CF645910
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|67014256|gb|CO443005.1|CO443005
EST:     CTGTTAAAA-GAATG-AATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|50323940|gb|CO519066.1|CO519066
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|26558362|gb|CA830597.1|CA830597
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGTCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|87157289|gb|DY402078.1|DY402078
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGTCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|71770543|gb|DR968480.1|DR968480
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|91872707|gb|EB402664.1|EB402664
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|22472216|gb|BU036696.1|BU036696
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGTCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|91877955|gb|EB407912.1|EB407912
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
EST: gi|50337086|gb|CO532212.1|CO532212
EST:     CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAG                         TACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA
genomic: CAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACA

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: 47 (upstream exon), 41 (downstream exon)
Score: 38

GCACAACTATGGTCTTGATTTGTTCCTTTTATCTGTCGATGAAGGAATCACAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT


Block sizes: 42 (upstream exon), 41 (downstream exon)
Score: 39

GCACAACTATGGTCTTGATTTGTTCCTTTTATCTGTCGATGAAGGAATCACAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 47

GCACAACTATGGTCTTGATTTGTTCCTTTTATCTGTCGATGAAGGAATCACAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT


Block sizes: 40 (upstream exon), 41 (downstream exon)
Score: 23

GCACAACTATGGTCTTGATTTGTTCCTTTTATCTGTCGATGAAGGAATCACAGGATATAGAGATGACTCACTAGAAACTGTTAAAAGGAATGAAATACAGgtctcccggt ... cctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatattttagtgtgtggtatttggattcagtgagtttcactattccctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT
                                  tttcactattccct  CT-rich tract
                 tattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcccggtcacagacacacttgctcagttttctggaagctctgactttaaatattttagtgtgtggtatttggattcagtgagtttcactattccctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA