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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatgggaatggtcacattaattacctttatctgtaagcctgtcaccataaagccctactaaaatactctctcgactgaagcaaattttttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG

Basic information

species Zea mays
transcript GRMZM2G171688_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 3'ss of exon 3
taaaatgggaatggtcacattaattacctttatctgtaagcctgtcaccataaagccct--actaaaatac-tctctcgactgaagcaaattttttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG
|||      |||||      ||||    | ||    | | |   | ||  ||     ||  ||||||  || | | | | ||||  |||| || |||  |||||||||||| || ||||| ||| |||||||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||| ||||||||| |||
taaggcaa-aatgga-gtggtaatgggatctagtaatta-ctaattactgtatgttacttgactaaacaacctatgtggtctgagacaaacttctttcactagATATCTCCTCGCCAAGGACTTCTGAGAGTCCGAGAATTTACTTTAGCGGAGATTGAGCACTTTGTGGACCCAGAGGACAAATCCCACCCAAAGTTTCGTG

upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 1
-taaaatgggaatggtcacattaatt--acctttatctgta--agcctgtcaccataaagccctactaaaatactctctcgactgaagcaaattttttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG
 |    |    ||  ||     ||||    |||||| | |   |  || ||   || |              |     | |  || |     ||| | |   ||||||||||| || || || ||| ||||||| || ||||| || || ||||| |||||||||||||| |||||    || || || ||||| ||||    ||
gtgggttcatgattttcgtggcaatttagactttattttttttatactttctaaattagatatagtctttgcatgaattgggttggatgttgtttgtgtgtttagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAGATTGAGCACTTTGTTGACCCTCTAGATAAGTCTCATCCCAAGTACCCTG

upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 3
--taaaatgggaatggtcacattaattaccttta-tctgtaagcctgtcaccataaagccctactaaaatactctctcga-ctgaagcaaattttttttg---ctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG
  |    |     |||||    |  |||| | || | || | | || || || ||    || |  ||   || |  |  | ||||     ||||  ||       ||||||||||||| ||||||||||||||||| || ||||| || || || || |||||| ||||||| || || || |||||||| || || || | |  ||
ttttggttctttttggtcttggt--ttacttataatttggagggctatctccttag---ccga--aatgcacacattaaatctgataatgatttccttaaagttcagATATCTCCCCGCCAAGGCCTTTTGAGAGTTCGCGAGTTCACATTGGCAGAGATTGAGTACTTTGTTGATCCTGAAGACAAATCTCACCCCAAATATTCTG

upper sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 3
--taaaatgggaatggtcacattaattacctttatctgtaagcctgtcaccataaagccctactaaaatactctctcgactgaagcaaattttttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG
   |        |||   |   ||  |    |       | || |  |||  | | |      | ||       |  | |   | | | || |   ||| |||||||||| || ||||| || || ||||| ||||| |||||| | || || ||||||||||||||||| || || ||||| || || ||||| |||  ||
tccatctcaatgatgcctattctacatgatatctaaaacatgctttgcactgtgatggtgagttgaa-cctgaacatggcattatccatttatgaatgc-agATATCTCCACGCCAAGGTCTCTTAAGAGTTCGTGAATTTACTCTGGCTGAGATTGAGCACTTTGTGGATCCTGATGACAAGTCTCACCCAAAATTTTCTG

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|31356439|gb|CD440796.1|CD440796
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
EST: gi|148972573|gb|EE023537.2|EE023537
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAG-CCTTTTGAGAGTCCGTGAGTTTACTTT
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTT
EST: gi|211446351|gb|FL194325.1|FL194325
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
EST: gi|13126604|gb|BG317174.1|BG317174
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
EST: gi|60342069|gb|DN209042.1|DN209042
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
EST: gi|211446352|gb|FL194326.1|FL194326
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAGG
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGG
EST: gi|47961805|gb|CN844514.1|CN844514
EST:     AAGCTGCCATTCGCTGCAGCCCAAATTGGNTCAGGCCTTCAGGGAATGAG                         ATATCTCCC-GTCNAGGCCTTTTGAGA
genomic: AAGCTGCCATTCGCTGCAGCCCAAATTGG-TCAGGCCTTCAGG-AATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGA
EST: gi|31354132|gb|CD438489.1|CD438489
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
EST: gi|211446355|gb|FL194329.1|FL194329
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
EST: gi|211446353|gb|FL194327.1|FL194327
EST:     ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAG                         ATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA
genomic: ATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAA

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: 281

AGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

AGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

AGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

AGCTCAGGGTATATTTGTGAACTTCAAAGACTTGTATTACTACAATGGCAATAAGCTGCCATTCGCTGCAGCCCAAATTGGTCAGGCCTTCAGGAATGAGgcatgacttt ... tttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccataaagccctactaaaatactctctcgactgaagcaaattttttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG
             tactaaa  putative branch site (score: 207)
                                          ttttttttgct  putative PPT
                                   aagcaaatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatgggaatggtcacattaattacctttatctgtaagcctgtcaccataaagccctactaaaatactctctcgactgaagcaaattttttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - -gtcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaagc