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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACTGCTTCCCGCCTCTCGCCCCCGCGCTTCAGCACCCCTTCCCCGTCTCTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgtctttgcccccccgcgcgtctgccttgactctgttgctcggatattctcagatgtctggggaggctggagtaatgtttgcatcactaattt...

Basic information

species Zea mays
transcript GRMZM2G003096_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003096_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g07090.1 (Oryza sativa), 5'ss of exon 1
CCACTGCTTCCCGCCTCTCGCCCCCGCGCTTC--AGCACCC-CTTCCCCGTCTCTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgtctttgcccccccgcgcgtctgccttgactctgttgctcggatattctcagatgtctggggaggctggagtaatgtttgcatcactaattt--
   ||||| ||||||||||||| || ||| ||   |||||| || |||| ||||  ||||  ||    ||||||||||||||||||||| ||||||| |||||||| | |   ||     | || |  ||     |||  || ||    |  ||||   |     |||   | |   |   ||  | |     || |   ||   
---CTGCTACCCGCCTCTCGCCGCCTCGCCTCCACGCACCCACTACCCCTTCTCCCCATCTCCCGCTTCGCCGCTCGCGCTTCTCCCCTCTTCGCGCCGCCAAgtatgcctccctgcttacacctgttcgatcctcttatctttgcccttacgataagtttca--gtccacgaaatgttcggttttatcgaattctcgggttcct
















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|211152125|gb|FL081699.1|FL081699
EST:     CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAA                         GTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
genomic: CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
EST: gi|211152122|gb|FL081696.1|FL081696
EST:     CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCA-SCAA                         GTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
genomic: CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
EST: gi|211152126|gb|FL081700.1|FL081700
EST:     CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAA                         GTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
genomic: CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
EST: gi|60352390|gb|DN219363.1|DN219363
EST:     CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAA                         GTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
genomic: CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
EST: gi|211236843|gb|FL081704.1|FL081704
EST:     CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAA                         GTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
genomic: CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
EST: gi|211152129|gb|FL081703.1|FL081703
EST:     CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCCA                         GTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA
genomic: CTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAA

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: 42 (upstream exon), 47 (downstream exon)
Score: 27

CCACTGCTTCCCGCCTCTCGCCCCCGCGCTTCAGCACCCCTTCCCCGTCTCTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 93

CCACTGCTTCCCGCCTCTCGCCCCCGCGCTTCAGCACCCCTTCCCCGTCTCTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAAG


Block sizes: 28 (upstream exon), 41 (downstream exon)
Score: 4

CCACTGCTTCCCGCCTCTCGCCCCCGCGCTTCAGCACCCCTTCCCCGTCTCTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 25

CCACTGCTTCCCGCCTCTCGCCCCCGCGCTTCAGCACCCCTTCCCCGTCTCTTCATCCTCCAAACCGCCGCTCGCGCTTCTCCCCTGTTCGCGCAGCCAAgtacggccgt ... gtcattgtagGTTGGAAGCTGTGCTGTCTATTGGTGCTCATCTAATCCCACACCCAAGAAAG