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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaagttatattgcatagtcaatccatgttttgtcgtcttggtcaccgtaaatagactagggtttctttagttctattaggatctaagtgcttattctctttctttag

Basic information

species Zea mays
transcript GRMZM2G044237_T04
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 14
CAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaagttatattgcatagtcaatccatgttttgtcgtcttggtcaccgtaaatagactagggtttctttagttct---attaggatctaag-tgcttattctctttctttag
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CTGTCGGTTATTCAGGCATTCAGTTTGATGCGGACCAGCTTGATATTTCCCTTGGAGCTATTCCACTAATGAAAAATGGTCAACCACTCCCATTTGACAGgttaagaaaccttg-acaacatag--aattattttttt----tattgacgactttgaatgaattgtaatttgtgtagatcttacaatagaatttaaaatatctactgtttcttcatag
















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|74242072|gb|DT649986.1|DT649986
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|32934567|gb|CF039379.1|CF039379
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGT
EST: gi|32835096|gb|CD974774.1|CD974774
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTA
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTA
EST: gi|78092274|gb|DV520648.1|DV520648
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|148938789|gb|EC883127.2|EC883127
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|32928445|gb|CF033257.1|CF033257
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGT
EST: gi|76917242|gb|DV166726.1|DV166726
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|211349360|gb|FL434476.1|FL434476
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
EST: gi|78027443|gb|DV495830.1|DV495830
EST:     CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAG                         ATTGGCCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT
genomic: CTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGT

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: 29 (upstream exon), 49 (downstream exon)
Score: 6

CAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTG


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 6

CAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 10

CAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTG


Block sizes: 8 (upstream exon), 42 (downstream exon)
Score: 5

CAGTTGGTTATTCAGGCATTCAATTTGACGCAAATCGACTTGATATTTCTCTGGGAGTTATTCCACTAATGAAAAATGGGCAACCACTCCCCTTTGACAGgttagacaaa ... ctttctttagATTGACCGCTAGCAAGTATCTCAAAGATGCTGGAGATGCCCATGGTACAGTAAACATTGATATATCAGTTG