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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT

Basic information

species Zea mays
transcript GRMZM2G076049_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
gtacgtgcaccgacccagtccgactaataaatcactctctatag-ttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
|| | || | ||||| ||| | || | | || ||| | ||||||| | ||||| | | | | || | ||||| ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||
-----------------------gtacgtattctcgtcctataacttggcgttaagaatgtac--tactggtgaagcagcat---tgtgatttgtga-gtaacctgctgtggccgcgtg-tagGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
| | | ||| | | | | | |||| | ||| | || | | | |||| || || | |||||||| ||| |||||||||||||||||||| || ||| | ||||||||||| ||||||||||||||| ||||| | |||||||| || ||||||| |
------------------------------gtaagtttct-tgttctgttatgaaaatgtagattgatagagaa-tatgatgatgattaatgaggtaggcacattgtgttgtttact--cagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
||| | ||| | | ||| | | || ||| | || | | | | |||| || | | |||||||| ||| ||||||||||||||||||||| |||||| | ||||||||||| |||||||||||| || |||| | |||||||| || ||||||| |
--------------------------gtaagtttttctgttttgtt---------ctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttct--cagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgtgcaccgacccagtccgactaataaatc-actctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
||| || ||||| | | | ||| || | | || || | | | | || | || |||| | ||||| || | |||| || |||||||||||||| |||||| | |||||||| || |||||||||||||| | ||| | | || ||| | | ||||| |
--------------------------gtaagtctactctactaacatacatttcaaact------tctccttcttctaa----tctctaacttttccgacgatatttcaaaa----atctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------gtacgtgcaccgacccagtccgactaataaatcac---tctctatagttgc---cttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgta-acagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
||| ||| || | | | | || | | | | || ||||| | | | || || || ||| | | ||| | | | ||| | | | | ||||| ||| ||| ||||||||||||||||| || |||||||| ||||||||| | || ||||| |||| | | | |||| ||||| | | || |
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgct-gaaat-tgtaaaattgaccttgacgat-ggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
| || | | | | | | | || | | || | | | || | |||| ||| || |||||| |||| || ||||| |||||||| | ||||||||||| ||||| || |||||||||||||||||| ||||| |||||||| || || | || |
---------------------------------gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctag------tcgatcgattt--tcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT

upper sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ08014 (Selaginella moellendorffii), 3'ss of exon 1
gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
| |||| | ||| | | | | | || | | | | | || | |||| ||| || |||||| |||| || ||||| |||||||| ||||||||||||| ||||| || |||||||||||||||||| ||||| |||||||| || || | || |
-----------------------------------gtaccatagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttc----tagtcgatcgattt--tcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCCGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT

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|5268634|gb|AI770598.1|AI770598
EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
EST: gi|211132427|gb|FL330812.1|FL330812
EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGAG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
EST: gi|211531487|gb|FL328402.1|FL328402
EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
EST: gi|5268673|gb|AI770637.1|AI770637
EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
EST: gi|71762692|gb|DR960629.1|DR960629
EST:     GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGG                         GTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG

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 2 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 80

CATCCTCTTCTTCGAGGGGCAGCGCTCGGGGAGGCTCCCGCCGGACCAGCGCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT


Block sizes: 16 (upstream exon), 34 (downstream exon)
Score: 1

CATCCTCTTCTTCGAGGGGCAGCGCTCGGGGAGGCTCCCGCCGGACCAGCGCCTCCGCTGGCGCCGCGACTCCGGCCTCCACGACGGCGCCGCGGCCGGGgtacgtgcac ... cgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT




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