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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttattttctgtgttggcttaggatgctattaccacttgcatccagatcacaaaaccaaacccattccgtaattctgtcaccactttatccag

Basic information

species Zea mays
transcript GRMZM2G409430_T02
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409430_T02 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os01g54240.2 (Oryza sativa), 5'ss of exon 16
CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttattttctgtgttggcttaggatgct-attaccacttgcatccagatcacaaaaccaaacccattccgtaattctgtc---acca----ctttatccag-------------------------
|| |||| ||| || || ||||||||||||||||||||||| ||| ||||||| |||||||  || |   | ||||  ||| || || | |  |   |    | | | |||           ||  |||  |||||   ||   | ||     || || | |                         
CTGATGAGAAATCCTTCTACACCTCAACGTTTCTGGCTACCACTTTTACATGACTCGgtaagctagtca-tatgtttacttggggtgttcagcaaagcagctagctaaatcttctttttgcccctgttcaataatttaatctgtatcaggcttttgattctgtttctatccccggttgtttctgcag
















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|33094907|gb|CF054901.1|CF054901
EST:     AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG                         GTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
genomic: AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
EST: gi|71423078|gb|DR805944.1|DR805944
EST:     AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG                         GTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
genomic: AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
EST: gi|211103891|gb|FL455672.1|FL455672
EST:     AAAAGCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG                         GTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
genomic: AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
EST: gi|211246515|gb|FL461040.1|FL461040
EST:     AAAACCCATCCACACCTCAACGTTTYTGGCTACCCCTTYTACATGATTCG                         GTGGAGCTACTTAATAGCAAACTCAGCCCTYTTATGGATGTTGCTGAGACG
genomic: AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
EST: gi|24766432|gb|CA401586.1|CA401586
EST:     AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG                         GTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
genomic: AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
EST: gi|7304511|gb|AW600450.1|AW600450
EST:     AAACCCATCCNCACCTCAACGTTTCTGGGCTACCCCTTCTACATGATTCG                         GTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
genomic: AAACCCATCCACACCTCAACGTTTCT-GGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
EST: gi|5929080|gb|AW056372.1|AW056372
EST:     AAAACCCATNNNNNNNTCAACGTTTCTGGCTACCCCTTCTACATGATTCG                         GTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
genomic: AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
EST: gi|71763805|gb|DR961742.1|DR961742
EST:     AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG                         GTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG
genomic: AAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACG

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), 48 (downstream exon)
Score: 84

CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACGACATTGTTGCTCAACAAGCTGCAAGAGCTGTCAATGGCCAAGCTGCGCC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 32

CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACGACATTGTTGCTCAACAAGCTGCAAGAGCTGTCAATGGCCAAGCTGCGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACGACATTGTTGCTCAACAAGCTGCAAGAGCTGTCAATGGCCAAGCTGCGCC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 25

CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCGgtaacttatt ... ctttatccagGTGGAGCTACTTAATAGCAAACTCAGCCCTCTTATGGATGTTGCTGAGACGACATTGTTGCTCAACAAGCTGCAAGAGCTGTCAATGGCCAAGCTGCGCC