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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaaactcagccaccggatgattattcccgtctcctttgcctctgctctgagtctcacgaaaggtggccggcccctttggcttttgtttctgaatgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG

Basic information

species Zea mays
transcript GRMZM2G129954_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129954_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g04720.2 (Oryza sativa), 3'ss of exon 1
gcaaactcagccaccggatgattattcccgtctcctttgcctctgctctgagtctcacgaaaggtggccggcccctttggcttttgtttctgaatgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG
    | |     |        || | |  |    || |     |     |  |        |  ||||         | | ||| | || ||  | | || ||| |||||||| || |||||||||||||| ||| ||||| |||| |||||||| || ||   ||       | ||   ||  |  | |||| |
--gtattacaagatttttcttttgtgcttgcagactcttttcttctctcggttgctgtatgaattggcatctgatggtaggtttggcttttg--tttgtgtagTTACCACTGTTGATTCCGGGAGCAAGGCTCTGGAGTTCTTGGGGCTCCATGATCATGAGGACAGCCCAATTTCTACTCAATCAGATCAGCAG

upper sequence: GRMZM2G129954_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g04720.1 (Oryza sativa), 3'ss of exon 1
gcaaactcagccaccggatgattattcccgtctcctttgcctctgctctgagtctcacgaaaggtggccggcccctttggcttttgtttctgaatgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG
    | |     |        || | |  |    || |     |     |  |        |  ||||         | | ||| | || ||  | | || ||| |||||||| || |||||||||||||| ||| ||||| |||| |||||||| || ||   ||       | ||   ||             
--gtattacaagatttttcttttgtgcttgcagactcttttcttctctcggttgctgtatgaattggcatctgatggtagGTTTGGCTTTTG--TTTGTGTAGTTACCACTGTTGATTCCGGGAGCAAGGCTCTGGAGTTCTTGGGGCTCCATGATCATGAGGACAGCCCAATTTCTACTCA-------------
















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|211012455|gb|FL207173.1|FL207173
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009674|gb|FL207158.1|FL207158
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009673|gb|FL207157.1|FL207157
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211012446|gb|FL207164.1|FL207164
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009675|gb|FL207159.1|FL207159
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|91878635|gb|EB408592.1|EB408592
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|40303893|gb|CK348280.1|CK348280
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009671|gb|FL207155.1|FL207155
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|19822364|gb|BQ048388.1|BQ048388
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211012448|gb|FL207166.1|FL207166
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009672|gb|FL207156.1|FL207156
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009678|gb|FL207162.1|FL207162
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009679|gb|FL207163.1|FL207163
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGAMCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|76933673|gb|DV173540.1|DV173540
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009677|gb|FL207161.1|FL207161
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|26455829|gb|CA827412.1|CA827412
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009676|gb|FL207160.1|FL207160
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|40335323|gb|CK369393.1|CK369393
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|91869452|gb|EB400392.1|EB400392
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|113704219|gb|EE681723.1|EE681723
EST:     CGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211012454|gb|FL207172.1|FL207172
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|74237752|gb|DT645666.1|DT645666
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211012453|gb|FL207171.1|FL207171
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGGCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211012452|gb|FL207170.1|FL207170
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211009670|gb|FL207154.1|FL207154
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211012447|gb|FL207165.1|FL207165
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATG
EST: gi|211012449|gb|FL207167.1|FL207167
EST:     CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAG                         TGACCACTGTCGACTCCGGGRNGCAAGGCGCTGCAGTTCCTGGGCCTCCAT
genomic: CCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGA-GCAAGGCGCTGCAGTTCCTGGGCCTCCAT

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: 38

GCGGTGGCCACAGAGACTCCGTTCCATGTCCTGGCGGTGGACGACAGCCTCCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149

GCGGTGGCCACAGAGACTCCGTTCCATGTCCTGGCGGTGGACGACAGCCTCCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

GCGGTGGCCACAGAGACTCCGTTCCATGTCCTGGCGGTGGACGACAGCCTCCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 32

GCGGTGGCCACAGAGACTCCGTTCCATGTCCTGGCGGTGGACGACAGCCTCCCGGACAGGAAGCTCATCGAGAGGCTCCTCAAGACCTCTTCCTTCCAAGgcaaactcag ... atgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtctcacgaaaggtggccggcccctttggcttttgtttctgaatgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG
   gtctcac  putative branch site (score: 32)
                                 ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaactcagccaccggatgattattcccgtctcctttgcctctgctctgagtctcacgaaaggtggccggcccctttggcttttgtttctgaatgtatgcagTGACCACTGTCGACTCCGGGAGCAAGGCGCTGCAGTTCCTGGGCCTCCATGACCAGGACAGCACGGTTCCTCCTGTCCACACGCACCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG