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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcgatcgatgccctcatttcttgctgctatcacgtttcttggccctcaattctgaacaagtgcaagcgacgctctctgtttccaacag

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 14
GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcgatcgatgccctcatttcttgctgctatcacgtttcttggccctcaattctgaacaagtgcaagcgacgctctctgttt------ccaacag
|||||||||||||||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||||||||||||| || ||         |  ||||| |  ||  | |   |  || | | || || |||||||||  ||||||| |  || | | |||      |||||||
GACATCAAGTTTGCTGTTCATGCACACCCAACATTGTCCGAGGTGCTGGACGAACTCTTTAAAGCAGCCAAGgtacacttcagcg-----ctccatttttctcttgtgtttagaatccttgaccacatttctgaacagctgcaagctattcttttttttttccttcccaacag

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 14
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 5'ss of exon 14
GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcgatcgatgccctcatttcttgctgctatcacgtttcttggccctcaattctgaacaagtgcaagcgacgctctctgtttccaa-cag--------------------------------
||||| || || || ||||| ||||| || ||| | ||||||||||| || ||||| |||||||||||||||||| |     | |  |  ||||||  | |      |    |   |||    || || |   | |||  |  |   | |  ||||  |   || ||                                 
GACATAAAATTGGCAGTTCATGCACATCCAACACTCTCTGAGGTCCTCGACGAACTGTTCAAAGCAGCCAAGgtaaa-gcaaaacagtctcctcatgccat-tgatcagagagcccctttattcttaactgcaatcaatag--atttaagtcctctactaaaaagcaaaagaatcttacactataagttcaatttttcag

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 14
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 14
GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcgatcgatgccctcatttcttgctgct-atcacgtttcttggccctcaattctgaacaagtgcaagcgacgctctctgtttcca-acag---
||||| |||||||||||||| ||||| || || ||||| ||||| || || |||||||||||| | || ||||||  |     |      |   |   |   ||| |   |  |||  ||     | ||   | || |  |   |  |      | ||||  || |||    
GACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAGgtaagctcttctttccctctatagacccctctgatcgacctgttaattcattataaagatttaatagattggaaagggagaatatgttgtcatacatagc

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|32944152|gb|CF048971.1|CF048971
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|67029833|gb|CO458582.1|CO458582
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|211287326|gb|FL348627.1|FL348627
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|24767210|gb|CA402354.1|CA402354
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|16378693|gb|BI992557.1|BI992557
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|24769965|gb|CA405094.1|CA405094
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|31362407|gb|CD446764.1|CD446764
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|78075765|gb|DV504199.1|DV504199
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|211284887|gb|FL322128.1|FL322128
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|4885872|gb|AI676992.1|AI676992
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|60340265|gb|DN207238.1|DN207238
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|67018763|gb|CO447512.1|CO447512
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
EST: gi|31353176|gb|CD437533.1|CD437533
EST:     CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAG                         GTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA
genomic: CACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 150

GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGAAAGGCCGGATAGCAAGCCAAGGCAGCCACCCCAACCACTCCTGAAGGTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 151

GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGAAAGGCCGGATAGCAAGCCAAGGCAGCCACCCCAACCACTCCTGAAGGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 182

GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGAAAGGCCGGATAGCAAGCCAAGGCAGCCACCCCAACCACTCCTGAAGGTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 243

GACATCAAGTTTGCTGTTCACGCACACCCTACATTGTCTGAGGTCCTGGATGAACTCTTCAAAGCAGCCAAGgtatacatcg ... tttccaacagGTTAATTCCGGTGTTTCTCATTCTGTAAATGAACCAGTTGCAGCCTAGAGAAAGGCCGGATAGCAAGCCAAGGCAGCCACCCCAACCACTCCTGAAGGTC