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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcgaaagacgtagattctttcatttgtgcatggatgtgctgatgtgctgtgcttctgtgtacgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTGGGGCATGCATGGCGTCGGACAACTGCGCCAACGTGTGCCGCGGTGAGGG

Basic information

species Zea mays
transcript GRMZM5G896902_T01
intron # 1
splice site 3'
intron type U2

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|22545140|gb|BU097499.1|BU097499
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|7145283|gb|AW506764.1|AW506764
EST:     GTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: GTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|116828993|gb|EC863039.1|EC863039
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|7137640|gb|AW499196.1|AW499196
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|116826333|gb|EC870115.1|EC870115
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|116826415|gb|EC870197.1|EC870197
EST:     CATGTACCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|32869622|gb|CF009304.1|CF009304
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|7145281|gb|AW506762.1|AW506762
EST:     ATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: ATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|21480929|gb|BQ577612.1|BQ577612
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|116813364|gb|EC855802.1|EC855802
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|21329765|gb|BQ485132.1|BQ485132
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
EST: gi|8577156|gb|BE129793.1|BE129793
EST:     CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCG                         ATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG
genomic: CATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTG

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: 15 (upstream exon), 42 (downstream exon)
Score: 2

TGCATATATATATATAATCCTGCCAAGACAAAGGTAATGGAGTCGTCACGCATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTGGGGCATGCATGGCGTCGGACAACTGCGCCAACGTGTGCCGCGGTGAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1098

TGCATATATATATATAATCCTGCCAAGACAAAGGTAATGGAGTCGTCACGCATGTTCCAGCCGGCCATCATCCTGCTTCTCCTGCTCATTGTGACCACCGgtatgttcga ... cgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTGGGGCATGCATGGCGTCGGACAACTGCGCCAACGTGTGCCGCGGTGAGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcatttgtgcatggatgtgctgatgtgctgtgcttctgtgtacgtgctttagATGTGGCGCAGGCGGCGAGGGAATGCGAGAAGGACAGCGAGCGATTCCTTGGGGCATGCATGGCGTCGGACAACTGCGCCAACGTGTGCCGCGGTGAGGG
                    tgctgat  putative branch site (score: 1098)