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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAAGATCTTAGCAAATGCTGATGGACTTCGGTTGCTGCGCACACTGGAAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactggtaaccacaaaattctaagaatatctgcaagcatgatgtaatcgatccttgtttatgcag

Basic information

species Zea mays
transcript GRMZM2G030422_T03
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T02 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 17
TATCAAGATCTTAGCAAATGCTGATGGACTTCGGTTGCTGCGCACACTGGAAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactggtaaccac--aaaatt----ctaagaatatctgcaagcatgatgtaatcgatccttgtttatgcag
|||||||||||||||||||||||||||| | ||||||||||||||| ||||||||||||| |||||||||||||| | ||| |||||| ||||||||||||||| | || || ||||   ||||||    ||||  || | ||||||| |||   ||| ||||| | ||  |||||
TATCAAGATCTTAGCAAATGCTGATGGAGTACGGTTGCTGCGCACATTGGAAAATCGTTCATTTGATGCTTCTCGGAGTGCGTCTGAGACTGTAACAAAGgtaagttcttgtgaccatttaaaattacaactaaatatttttgcaagcttgacccaatagatccatcttggtgcag
















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|87156341|gb|DY401130.1|DY401130
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|211268556|gb|FL032964.1|FL032964
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|32793640|gb|CD945876.1|CD945876
EST:     AAAATCGGTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCTTTGACTGCTGCGGCAAATGCAGGTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|22490238|gb|BU050161.1|BU050161
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|211270985|gb|FL032966.1|FL032966
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|31360139|gb|CD444496.1|CD444496
EST:     AAAATCGTTCTTTTGATGCTTCTTGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|87152395|gb|DY397184.1|DY397184
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|211270984|gb|FL032965.1|FL032965
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|26559138|gb|CA831373.1|CA831373
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTG
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTG
EST: gi|19058659|gb|BM737326.1|BM737326
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAAG
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGC-AG
EST: gi|22520900|gb|BU079711.1|BU079711
EST:     AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAG                         CCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGT
EST: gi|31356149|gb|CD440506.1|CD440506
EST:     AAAATCGTTCTTTTGATGCTTCTTGCAATGCATCTGAGGCTGAAACAAAG                         CCTCTAATAAATCCCTTGACTG
genomic: AAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTG

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 9

TATCAAGATCTTAGCAAATGCTGATGGACTTCGGTTGCTGCGCACACTGGAAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGTTCAGGAGCTGGTGCTCCGTCAGCTATAACTGCAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 2

TATCAAGATCTTAGCAAATGCTGATGGACTTCGGTTGCTGCGCACACTGGAAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGTTCAGGAGCTGGTGCTCCGTCAGCTATAACTGCAATG


Block sizes: 29 (upstream exon), 21 (downstream exon)
Score: 1

TATCAAGATCTTAGCAAATGCTGATGGACTTCGGTTGCTGCGCACACTGGAAAATCGTTCTTTTGATGCTTCTCGTAATGCATCTGAGGCTGTAACAAAGgtaattactg ... gtttatgcagCCTCTAATAAATCCCTTGACTGCTGCGGCAAATGCAGCTGCAGCAAGCAGTTCAGGAGCTGGTGCTCCGTCAGCTATAACTGCAATG