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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

Basic information

species Zea mays
transcript GRMZM2G081462_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------------------------------------gtacgcacctacctta-----tctcttttcatccattcggg-gagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                             || ||  |    |||     ||  |||  |  || | | |  || |||||| |||||   |     ||||||   ||    ||| |||||||||||||||||||||||||| ||||||||||| |||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgct----gttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 2
gtacgcacctaccttatctcttt-----tcatccattcgggga-gaaattcagctgaaagtttcatgtgatttgca----ctca--------ctgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
||| | |    |||| |  ||||     | |   || |      ||  |||   |  |  | |  | ||   ||||    ||||        ||||  ||||| |||||||||||  | ||||| ||||| ||||| |||||| |||| ||| ||||||| ||||| || ||||| || |||||||| ||||| ||||||
gtatggaaacgccttgtgcctttaatttttaattatccttctttgattttctatttgatatcttgtttgtagtgcatgacctcattttgattctgtgcagGTTTTTGAACAAGGGTTTATCTGATTTCAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCAAAGTTTATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G30350.1 (Glycine max), 3'ss of exon 2
-------------gtacgcaccta--ccttatctctt-ttcatccatt--cggggagaaat-tcagctgaaagtttcatgtgatttgcactcactgttt-----------agGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
              |  ||   ||   ||||  |||  ||| | ||||  |     || || ||   |||| ||||  |||| | ||  |||| | |||           ||||| |||||||| ||  | ||||| || || ||||| |||||| |||| ||| ||||||| ||||| || ||||| || |||||||||||||| ||||||
gtatggacacaccttgtgcctttaattcttaattctcattctttcatttcctatttgatatctcgtttgaatgtttgttgtg-tatggcctcattattttgattctgtgcagGTTTTTGAACAAAGGTTTATCTGATTTTAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCCAAGTTTATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttca--tgtgatt-tgcactcactgtt-tagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
               |||||||  ||   |            || | || |  ||||||  | ||||  |  |||   | |   |||||||||||||||||  ||||||| ||||||||||| || ||  |||| |||||||| ||||| ||||| ||||| ||||||||||| || |||||||||
----------gtaagatctcttaacactaaggacctctctttttaatctaagtgtttcaattttgatgataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------gtacgcacc-taccttatct--cttttcatccattcggggagaaattcagct--------gaaagtttcatgtgatttgcactcactgtt----tagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                              || ||| | ||  ||      |   | || ||   |  |||   |  ||||         ||||| | |  | |  | ||    ||| |     || ||  ||||||| ||  | ||||| ||||| |||||  ||||| |||||||||| || |||||||| ||||||||||| || ||||||||||||||||||
gtatgcaaacaactctctgcccttctcccttcctcactcatggtcatatgcatcatagtttgcagaacaagtaatacagctgttgagttttatagcttttaactgaaaagtctgaaataaacttcatgttctgctgttgcagATTTCTGAACAAAGGTTTATCTGATTTCAATTTGGCTTTGGACTTGGGGTTCCTCACAAAGGCTAGAAAGTACACCTTTTTTAAGCCCAAGTTCATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: EDP04035 (Chlamydomonas reinhardtii), 3'ss of exon 4
--gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatg----tgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTC--TGACTT-CAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC---------
  ||  ||| |  | |     |   |   ||   |       ||  ||||   |   | ||        |    ||||| | |   | |  |    ||| |   |||    || ||  | |   ||| |   ||   || ||||||| ||||||   |  | ||  |  | |    |   |  |   ||||         
cggtcggcaacggcgtccctgcgcctttgcccacctcaccccaacccagcctcaccctccaccgcctcaaccctcactccccggcaacgcaccaacacagGTTCCTGCTCATGTCTCGCGATGAGGCCCGCCACGCCGGCTTCCTGAACAAGGCCCTGTCGGACTTCAACCTGGCCCTGGACCTGGGCTTCCTGACCAAG

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S97_248V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatgtgat-ttgcactcactgttt---agGTTCTTGAACAAGGGGCTG--TCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTT---CAAGCCCAAGTTCATCTTC-------
    | |   | ||   |  | ||   | |   |   |       |   ||   |  |   ||| || ||| | |  ||   |   | |    ||||||   | |     |||   |      |    |   |||   ||    |    | || ||  |      ||||||   ||||     ||    ||||       
agaaatgttgccactccaattgttgcaaacagcttttgatctttcttctctccgatatgattgtaatgttgaaattgcttccttccatgaatgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAAGCCAGACATGCTGGCTTCTTGAACAAGGGACTGTCAGACTTCAACTTGG

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ28505 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------------gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCT-GACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC--------------------------------------------------------------
                                          ||                                                                                                      ||||| |||||||| ||||| || || || |||||||| ||  ||||||||||||||||||||||  |||||||||||                                                              
gttctcagttactcagctggaaaaaaagcatcgatcatttcctatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgactttaacttggctctggatcttggatttctgaccaaagCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTCTACGCGACGTATCTCTCGGAGAAGATCGGCTACTGGAGGTACATTACTATCTACAGGCACTT

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ30397 (Selaginella moellendorffii), 3'ss of exon 2
gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                |   || |||     || |   ||||   |||    |   |||| |  | |    |||     ||||||| ||||||| ||  | || ||||| |||||||| ||||| || || || |||||||| ||  ||||||||||||||||||||||  |||||||||||
---------------gtaagttctcagtttctcagttggaaaaaaagcatcga---tcatttcctatatgttca-----tagGTTCCTGAACAAAGGATTATCCGACTTTAACTTGGCTCTGGATCTTGGATTTCTGACCAAAGCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTC

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|78112391|gb|DV530785.1|DV530785
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|84969707|gb|DW468136.1|DW468136
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|76016942|gb|DT944112.1|DT944112
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|78107168|gb|DV525586.1|DV525586
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|15323476|gb|BI478494.1|BI478494
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTGGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|211408498|gb|FL069298.1|FL069298
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCAGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|50325243|gb|CO520369.1|CO520369
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|13557965|gb|BG549321.1|BG549321
EST:     TCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GCTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGT
genomic: TCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagG-TTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGT
EST: gi|149097284|gb|EE183107.2|EE183107
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT

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), 48 (downstream exon)
Score: 149

AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1123

AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 17

AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 749

AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattcggggagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                         cactcac  putative branch site (score: 749)
          agaaatt  TA-rich tract