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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcaatcttcatttgcctacgcatcattctactttctgcattataattcagctgaagctcttttgacttttttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTGTAAGGATTCTGTGAACATAGACATTGTCATCGACTGGCTTATCAAGCAC

Basic information

species Zea mays
transcript GRMZM2G089454_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089454_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g49980.1 (Oryza sativa), 3'ss of exon 5
gtgagctcaat-cttcatttgcctacgc--atcattct---------actttctgcattataattcagctgaagctcttttgacttttttgt-tttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTGTAAGGATTCTGTGAACATAGACATTGTCATCGACTGGCTTATCAAGCAC
||||| | | | | | | || | || |||| || | || ||| || || |||| |||||| | || | | ||| |||||| || ||||||| |||||||||||| |||||||| |||||||||||||| || ||||| ||||| |||||||| ||||||| || |||||||||||||||
gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctt---tctcatgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCAC

upper sequence: GRMZM2G089454_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g49980.2 (Oryza sativa), 3'ss of exon 5
gtgagctcaat-cttcatttgcctacgc--atcattct---------actttctgcattataattcagctgaagctcttttgacttttttgt-tttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTGTAAGGATTCTGTGAACATAGACATTGTCATCGACTGGCTTATCAAGCAC
||||| | | | | | | || | || |||| || | || ||| || || |||| |||||| | || | | ||| |||||| || ||||||| |||||||||||| |||||||| |||||||||||||| || ||||| ||||| |||||||| ||||
gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagTGGTCTT---TCTCATGTATTTCAGAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGT----------------------

upper sequence: GRMZM2G089454_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0006g01090.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------gtgagctcaatctt-------catttgcctacgcatcattctactttctgcattata-attcagctgaagctcttttgactttt-----ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTGTAAGGATTCTGTGAACATAGACATTGTCATCGACTGGCTTATCAAGCAC
| | ||| | || |||||||| || | ||| | ||| | || | | | |||| || | |||||||| | || | || || | | | || || |||||||||||||||| || |||||||| |||||||||||| |||| || || ||||||||||| |||
gtgagttcagaaccagacgagttttcaataaaatcatttttgatatactatttgcctcgatggcaaacctttttttatattttgtgttttgacatattttttttcctccttggtggtggttttcagAGATCTCAAGTCAATCACAGGTAGAGAGGTGGGTTGCTACATGATCTCGTGCAAGGATTCCGTGAACATAGACCTTGTAATTGATTGGCTTATCAAACAC

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|5762129|gb|AI967177.1|AI967177
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCATTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
EST: gi|211225167|gb|FL467880.1|FL467880
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCATTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
EST: gi|5846814|gb|AI999897.1|AI999897
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCATTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
EST: gi|5296277|gb|AI783047.1|AI783047
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCATTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
EST: gi|211128977|gb|FL358619.1|FL358619
EST:     AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACT                         TGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
EST: gi|78022702|gb|DV491089.1|DV491089
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCATTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG

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 1 RNA-Seqlibrary.


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 4

TGCTGACAAAACAGTCTTTAGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTGTAAGGATTCTGTGAACATAGACATTGTCATCGACTGGCTTATCAAGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctactttctgcattataattcagctgaagctcttttgacttttttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTGTAAGGATTCTGTGAACATAGACATTGTCATCGACTGGCTTATCAAGCAC
                                  ttttgac  putative branch site (score: 4)
 ctcttttgactttttt  CT-rich tract
 attataattca  TA-rich tract