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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCCCTTTTCAAGTTCTCACAGTTCAACCAAAGTTCAAAACTCAAGTGCTAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttcttctatactcacgaaattagttgtttattaacttttaagttagtttttttattctaacaagaagtttcaagtttgtatttagaggtattatgttcaaagatttctcttaaaaacgactgtcgtgtgtacag

Basic information

species Zea mays
transcript GRMZM2G177001_T01
intron # 7
splice site 5'
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|5762181|gb|AI967229.1|AI967229
EST:     CCTGGCCCCCAAATAGAGG                         GTCCTCCTGGAGCCAATTTGTTCATATNCCNCATCCCGCAAGAATTTGGTG
genomic: CCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
EST: gi|26457270|gb|CA828853.1|CA828853
EST:     TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGG                         GTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
genomic: TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
EST: gi|71759776|gb|DR957713.1|DR957713
EST:     TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGG                         GTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
genomic: TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
EST: gi|78544274|gb|DV621772.1|DV621772
EST:     TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGG                         GTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
genomic: TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
EST: gi|89761503|gb|DY689493.1|DY689493
EST:     TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGG                         GTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
genomic: TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
EST: gi|21391157|gb|BQ529206.1|BQ529206
EST:     TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGG                         GTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
genomic: TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
EST: gi|32849977|gb|CD989658.1|CD989658
EST:     TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGG                         GTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
genomic: TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
EST: gi|32910410|gb|CF015222.1|CF015222
EST:     TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGG                         GTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG
genomic: TAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTG

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: 47 (upstream exon), 49 (downstream exon)
Score: 86

CGCCCCTTTTCAAGTTCTCACAGTTCAACCAAAGTTCAAAACTCAAGTGCTAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTGACCATGATCTTGCCAGTGCATTCCATAGTTTCGGTAGGGTACTGAGCGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 55

CGCCCCTTTTCAAGTTCTCACAGTTCAACCAAAGTTCAAAACTCAAGTGCTAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTGACCATGATCTTGCCAGTGCATTCCATAGTTTCGGTAGGGTACTGAGCGC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 21

CGCCCCTTTTCAAGTTCTCACAGTTCAACCAAAGTTCAAAACTCAAGTGCTAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTGACCATGATCTTGCCAGTGCATTCCATAGTTTCGGTAGGGTACTGAGCGC


Block sizes: 35 (upstream exon), 47 (downstream exon)
Score: 21

CGCCCCTTTTCAAGTTCTCACAGTTCAACCAAAGTTCAAAACTCAAGTGCTAATTCGCCGTCTTCGAGTCCCAGCAGCAATCCTGGCCCCCAGATAGAGGgtttgctttc ... gtgtgtacagGTCCTCCTGGAGCCAATTTGTTCATATACCACATCCCGCAAGAATTCGGTGACCATGATCTTGCCAGTGCATTCCATAGTTTCGGTAGGGTACTGAGCGC