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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggtctaccattgtttccttctttttcatcatggatgcatttctttttctttctttctgaacttatgttttcttgatttttattgtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG

Basic information

species Zea mays
transcript GRMZM2G404855_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g16900.2 (Oryza sativa), 3'ss of exon 3
gtttgtggtctaccattgtttccttctttttcatcatggatgcatttctt--tttctttctttctgaacttatgtttt-cttgatttttattgtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG
|| ||| ||||| |||| | | || || | ||| ||| ||| || | || | || || ||||| | ||| | ||| || ||||| |||| || |||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||||||||||
gtctgtttgctacc--tgttccttctaacttgatg--gaatgtattccttaattcatatcactgggagctgatgttctgtttgttctttgttttactttcagTGCTGTCGTGAAGTGGCTGAGAAGTACCCTGAAATTGTATACGAGGAGGTCATCATTGACAATTGTTGTATGACG
















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|14204192|gb|BG837869.1|BG837869
EST:     CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|60355306|gb|DN222279.1|DN222279
EST:     CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|6166676|gb|AW144940.1|AW144940
EST:     CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|60354405|gb|DN221378.1|DN221378
EST:     CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|6166632|gb|AW144896.1|AW144896
EST:     CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|6952333|gb|AW424401.1|AW424401
EST:     CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|6195048|gb|AW147152.1|AW147152
EST:     CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
EST: gi|6827805|gb|AW331448.1|AW331448
EST:     CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAG                         TGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC
genomic: CGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTC

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: 71

AGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGGAAAGGGTCTCTGCGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 107

AGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGGAAAGGGTCTCTGCGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 84

AGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGGAAAGGGTCTCTGCGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 145

AGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGGAAAGGGTCTCTGCGATTCACAAGGCCAATATTATGAGGAAGACAGATGGTCTTTTCCTCAAGgtttgtggtc ... gtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttttctttctttctgaacttatgttttcttgatttttattgtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG
                               tcttgat  putative branch site (score: 145)
 ttatgttttcttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtggtctaccattgtttccttctttttcatcatggatgcatttctttttctttctttctgaacttatgttttcttgatttttattgtacttgtagTGTTGCCGTGAAGTGGCTGAGACGTACCCTGAAATTCAATACGAGGAGGTCATCATTGACAATTGTTGTATGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG