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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgatatacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA

Basic information

species Zea mays
transcript GRMZM2G135283_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
gtatg-gcatgatgaaaacgataa-aaaaaactagca---ggtgttgaacctgcttctt--gcat------------taaaaaccaaaggtttagtgatat------acttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
||||   | |||  | ||| |||  || | | ||||    |||||||   ||| |||||   |||            | |    ||||    ||   ||        ||    ||   | |||||||||||||| ||||||||||| ||||||||||||||||| || |||||||||||||| || ||||| ||||||||||||||||| ||||||||||| |
gtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
--------------------------------------------------gtatggcatgatgaaaac--gataaaaaaaactagcaggtgttgaacctgcttcttgcattaa----aaaccaaaggtt----tagtgatatacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
                                                  |||      |||   |    ||| || |  | |||   ||||||    | || ||||  || |    ||  || |  |      |||  |     |   | | |  || |  ||||||| | |||||||||||||||    ||||| || ||||| |||||||| || ||||| ||||| || |||||||| || ||||||||  | |
gtaagtatcctggagaaaataatttgacatttttgtttattttgatctctgtactctcggatttcattctgatcaatagga-tagtttgtgttg--tttcctacttgagttgatgtaaattcataaatcataacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------gtatggcatgatgaaaacgataaaaa-aaactagcaggtgttgaa-cctgcttct-tgcattaaaaaccaaaggtt----tagtgatatacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
                                                  |||      |||   |     |  || |   ||| | ||||||   ||  |||   |  ||  |||  || |  |      |||  |     |   | | |  ||||  ||||||| |  || |||||||||||    ||||| || ||||| ||||||||||| ||||| ||||| || |||||||| || ||||||||| | |
gtcaattccaaggaaaaagttctttgacatttttgtttattttaatttctgtactctcagatttcattctcatcaacaggatagtatgtgttgtttcccacttgaatttatgtaaattcataaatcataacagttgttcttctttcaatttgaagGTATTGTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGA

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctg--cttcttgcattaaaaaccaaaggttta-gtgatatacttaatattct-atagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
                   | || |||||  ||||    |||||||      | ||  ||| |     ||   || | || ||  | ||  | |  | | ||||| ||||||||||||| ||||| |||||    |||||||| |||||||| |||||||| || || ||||| || || || ||  | ||||||||  | |
---------------gtaaaaaagaaaaagaagcaaaatttgaaccaaaatgttttagatttatgtataatctttcacgtcattcatttgttgtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGA

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------------gtatggcatgatgaaaacgataaaaaaaactagca-----ggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgat-atacttaatat-tctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
                                                         |||   |       |  | |  ||    ||         | |  ||||| ||    ||  |||      |   |   ||    | |||||| |||| | |  ||||| ||||||| | ||| ||||||||||||   |||||||||||||| || |||||||| ||||| || || || ||| ||||||| ||||||||  | |
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcctactccattactgttttaagtgtctgcttcttttgttactgaacttgagg-ttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 9
-gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgata--tacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
  | |  |    ||   | | |       | |       |   ||     |   || ||||     || |  |||    ||   |   |   || ||| ||||  ||||||| | ||| ||||||||||||   |||||||||||||| || |||||||| || || || ||||| ||| ||||||| || |||||  | |
tttttccccaattggttatggtttctttcagttttgaaagcaaaattca-taagtgaattatctggcacacatttttcaatggttgaattccatcctacagGTGTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGACCACACAATCATACTATTTCTGGCTTAGCAGTTGCATTGA

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaac------ctgcttcttgcattaa-aaaccaaaggtt-tagtgatatac------------ttaatattctata--------gGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
                                         | |  | |||   | |    | |    | ||  |  | ||   |      |||||||||   |||   |||   ||||| || || |  ||            || ||| | ||||        |||| ||||||| | ||| ||||||||||||   |||||||||||||| || |||||||| ||||| || || || ||| ||||||| ||||||||  | |
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 1
-gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgat-atacttaatat-tctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
    |   ||     |  | |               | |  ||||| ||    ||  |||      |   |   ||    | |||||| |||| | |  ||||| ||||||| | ||| ||||||||||||   |||||||||||||| || ||| |||  ||||| || || || ||| ||||||| ||||||||  | |
tcactactatttattaggcaagtgtctgcttcttttgttactgaacttgagg-ttatattgttggacgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 9
-gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgat-atacttaatat-tctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
    |   ||     |  | |               | | |||||| ||    ||  |||          |   ||    | |||||| |||| | |  ||||| ||||||| | ||| ||||||||||||   |||||||||||||| || ||| |||  ||||| || || || ||| ||||||| ||||||||  | |
tcactactatttattaggcaagtgtctgcttcttttgctattgaacttgagg-ttatattgttggatgtggaactaacatttatactttatatatgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA

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|67042253|gb|CO468508.1|CO468508
EST:     TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAG                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
genomic: TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
EST: gi|14204327|gb|BG838004.1|BG838004
EST:     TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAG                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
genomic: TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
EST: gi|60397906|gb|DN230722.1|DN230722
EST:     TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAG                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
genomic: TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
EST: gi|60351519|gb|DN218492.1|DN218492
EST:     TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAG                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
genomic: TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
EST: gi|40336482|gb|CK370552.1|CK370552
EST:     AAGAAATAAATAAACAAGGAAAAGAG                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
genomic: AAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
EST: gi|60346600|gb|DN213573.1|DN213573
EST:     TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAC                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
genomic: TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
EST: gi|67024112|gb|CO452861.1|CO452861
EST:     TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAG                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
genomic: TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
EST: gi|37393418|gb|CF633973.1|CF633973
EST:     AAGAAAT-AAT-AACAAGGGAAAAGAG                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCT
genomic: AAGAAATAAATAAACAA-GGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCT
EST: gi|60349820|gb|DN216793.1|DN216793
EST:     TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAG                         GTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG
genomic: TGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTG

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: 180

TGTAGTGACTACCACTACTCACAAATCACTCCGTGGGCCACGTGGAGCCATGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 214

TGTAGTGACTACCACTACTCACAAATCACTCCGTGGGCCACGTGGAGCCATGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

TGTAGTGACTACCACTACTCACAAATCACTCCGTGGGCCACGTGGAGCCATGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 262

TGTAGTGACTACCACTACTCACAAATCACTCCGTGGGCCACGTGGAGCCATGATCTTTTACAGGAAGGGAGTCAAAGAAATAAATAAACAAGGAAAAGAGgtatggcatg ... tattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgcttcttgcattaaaaaccaaaggtttagtgatatacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
                                       acttaat  putative branch site (score: 262)
                            tttagtgatatactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctgcttcttgcattaaaaaccaaaggtttagtgatatacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT