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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaactactgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatgactactgtttcgagtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT

Basic information

species Zea mays
transcript GRMZM2G135447_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135447_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g56110.2 (Oryza sativa), 3'ss of exon 4
gtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaactactgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatgactactgtttcgagtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT
             || |    | ||    |  |  |    ||| ||||  ||  | |||   | |  |         |||||    ||||  ||  |  |             | | ||| | | ||||||| |||||||||| |||| ||  ||||||| |||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||| || 
------------gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaatgcgtgaaatttacgggg-------------ttgtgta-tgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC

upper sequence: GRMZM2G135447_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g56140.2 (Oryza sativa), 3'ss of exon 4
gtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaactactgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatgactactgtttcgagtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT
||| |  |  |  ||| |  | | ||||     || | | |  |||        | |||   | |  |       | |||||    ||||  | | |  |  |   |     |  |||       ||||||  |||||||||| |||| ||  ||||||| |||||||||| ||||||||||| ||||||||||||||||||| |||||||||||||||||||| || 
gtacgcacgcatatatatg-cttcccatttgatcaattcaaccacatt-----tttctgcaccaaactcgatcttatgaaaatgcgtgaacttctcgg-gtgtacatgtgtgtatgag-------cagGAGGTGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAGCAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC

upper sequence: GRMZM2G135447_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S235_27V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaactactgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatga--ctactgtttcgagtactc-ac-cagGAGACGGAGAAGATGGCGCTCGCAGAGACGAC-CGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT
                              | |   |  |||    |   || |   |      |   ||  || ||  |      |     | | || |    |  | |||||   | | |||| || ||||||| |||||| |  |  |  ||| | ||    ||| ||  |||  ||||| || |||||||||||||||||  |||| |||||||||||||     | | 
------------------------------aagttattttaaggagatatcacca--tagaaaaacaattaaaataatgacgctgcttgtcttctagaagttctaaccaactgtcaagtgcactctacacagGAGATGGAGAA-ACAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGAGCTGCGAGG

upper sequence: GRMZM2G135447_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
gtaagaccctacctatgtttcctt-----ccatccatgcattgctaatacaacggcaacta------ctgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatgactactgtttcga-gtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT
|| ||  |||   | |  || |||     |  ||  ||  |   |      | ||| | |       |  || || ||||        |        | |    |||  |   ||||   || ||||  || ||   |||||||   | |||  |   |||||  |  | |||||||||||||| |||||||||||||||||||| || |||||||| |||||||||||||| |||  | 
gtgagtacctttgtgttctttcttgttggcattctgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttcgttgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG

upper sequence: GRMZM2G135447_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
gtaagaccctacctatgtttcctt-----ccatccatgcattgctaatacaacggcaacta------ctgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatgactactgtttcga-gtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT
|| ||  |||   | |  || |||     |  ||| ||  |   |      | ||| | |       |  || || ||||        |        | |    |||  |   ||||   || ||||  || ||   |||||||   | |||  |   |||||  |  | ||||| |||||||| |||||||||||||||||||| || |||||||| |||||||||||||| ||   | 
gtgagtacctttgtgttctttcttgttggcattccgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttgacatttgcttcgctgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG

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|86465713|gb|DY232086.1|DY232086
EST:     AGAAGTTGCTGCACTGGTGGGAGCTGCACTACAAGTGGCCCTACCCTTCT                         GAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAG
genomic: AGAAGTTGCTGCACTGGTGGGAGCTGCACTACAAGTGGCCCTACCCTTCTgtaagaccct ... tactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAG
EST: gi|76017410|gb|DT944580.1|DT944580
EST:     AGAAGTTGCTGCACTGGTGGGAGCTGCACTACAAGTGGCCCTACCCTTTT                         GAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAG
genomic: AGAAGTTGCTGCACTGGTGGGAGCTGCACTACAAGTGGCCCTACCCTTCTgtaagaccct ... tactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAG

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 35

GGAGTTCTCCAAGAGGAAGAAGAAAGGGAAGCTCCCCAAGGAGGCGAGGCAGAAGTTGCTGCACTGGTGGGAGCTGCACTACAAGTGGCCCTACCCTTCTgtaagaccct ... tactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT


Block sizes: 41 (upstream exon), 28 (downstream exon)
Score: 3

GGAGTTCTCCAAGAGGAAGAAGAAAGGGAAGCTCCCCAAGGAGGCGAGGCAGAAGTTGCTGCACTGGTGGGAGCTGCACTACAAGTGGCCCTACCCTTCTgtaagaccct ... tactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagaaaaaaaatgaagcttttgatgcatgactactgtttcgagtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT
                   ttttgat  putative branch site (score: 3)
     aaaaaaaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaactactgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatgactactgtttcgagtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG