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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcagttttgagtgtcactgaactgtttcttcagtcatctgtggttccttcagtgttgttttcttttgccttcataatctttaatgacatattgctgcactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA

Basic information

species Zea mays
transcript GRMZM2G003734_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003734_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g14654.3 (Oryza sativa), 3'ss of exon 17
gttagtcag-ttttgagtgtcactgaactgttt-cttcagtcatctgtggttccttcagtgttgttttcttttgccttcataatctttaatgacatattgctgcactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA
||||||||| || |   |   ||   | |  ||  || |||| | |   |  |||| | || |||| || | |        ||  ||  |    ||  || |  ||||  |||||||||||||| || ||| ||||||||||||| || || |||||||||||||| ||||||||||| |||||
gttagtcagattgtctctacaacgagatttcttgttttagtcctttccagacccttaaatggtgttctcatct--------aactttctacagtatgctgttctactatgcagGAATCAAGAAGTAACTGGATTGGTATTACAAGGGCTCTACAGCTTATAGTTGATGTAAATGATACTGCAAA
















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|60358866|gb|DN225839.1|DN225839
EST:     ACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAG                         GAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
genomic: ACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
EST: gi|37399448|gb|CF637052.1|CF637052
EST:     ACATGCACTTATTATAC-ATCTGGAGAAGGCTGG-CTTCTTAAGAGGCAG                         GAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
genomic: ACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
EST: gi|60347475|gb|DN214448.1|DN214448
EST:     ACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAG                         GAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
genomic: ACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
EST: gi|60353462|gb|DN220435.1|DN220435
EST:     CTTAAGAGGCAG                         GAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
genomic: CTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
EST: gi|71440283|gb|DR821333.1|DR821333
EST:     ACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAG                         GAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
genomic: ACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
EST: gi|76292770|gb|DV032338.1|DV032338
EST:     TGGCCTTCTTAAGAGGCAG                         GAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT
genomic: TGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTT

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), 46 (downstream exon)
Score: 110

GCGGGAGATACTTCATAGTTATGGCTTTGAGCACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 102

GCGGGAGATACTTCATAGTTATGGCTTTGAGCACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GCGGGAGATACTTCATAGTTATGGCTTTGAGCACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 59

GCGGGAGATACTTCATAGTTATGGCTTTGAGCACATGCACTTATTATACAATCTGGAGAAGGCTGGCCTTCTTAAGAGGCAGgttagtcagt ... cactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgttttcttttgccttcataatctttaatgacatattgctgcactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA
                          ctttaat  putative branch site (score: 59)
                  ttcataatctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcagttttgagtgtcactgaactgtttcttcagtcatctgtggttccttcagtgttgttttcttttgccttcataatctttaatgacatattgctgcactacccagGAATCAAGAAGCAATTGGGTTGGTATTACAAGAGCACTGCAGCTTATAGTTGACGTAAATGATACAGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT