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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaatttctagtactaaagaagataccaataactgcttctcattcaatggtttggataattctttactaggtcctcacatataatttctgttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGCAAAGTTGGCACGGTGGGTACTAGCAGCTGAAGATATATGCTTTAAAAAT

Basic information

species Vitis vinifera
transcript Vv00s1546g00010.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s1546g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g57150.1 (Oryza sativa), 3'ss of exon 1
gttaatttctagtactaaa--gaagataccaataactgcttctcattcaatggt-ttggataattcttta--ctaggtcctcacatataatttctgttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGCAAAGTTGGCACGGTGGGTACTAGCAGCTGAAGATATATGCTTTAAAAAT
    ||   ||||  | ||  | |  |||   |  ||||||   |||     || ||||  | |||  ||  || |    |    |||| ||  |  | || |||| |||| |||||| | |||||||||||||||||||||||  | |  ||||| ||  |   | | |||||  |  |||| || || || ||||| |  |||
---gatggatagttatgaattggatgtacagttctctgcttaaaattggtctgtgttggccatttcaataaccttgaggttattctatacttgtt--tgtaccagGATGGATGACCCACTTATGTGGGGATTCAAGGGTTTTCCAACTACAGATGCCAAACTTCAAAGATGGGTGTTGACAGCAGAGGACATCTGCTTCAGGAAT

upper sequence: Vv00s1546g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G125083_T01 (Zea mays), 3'ss of exon 1
----gttaatttctagtactaaagaagataccaataactgcttctcattcaatggtttggataattctttactaggtcctcacatataatttctgttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGCAAAGTTGGCACGGTGGGTACTAGCAGCTGAAGATATATGCTTTAAAAAT
    ||   | || | |     |      | || |  ||   |    |||| | ||  | ||  | ||| |       ||    | || |  || || || |||||| || |||||  | |||||||||||||||||||||||  |   |||||||||| | | | ||||||| ||  |||| |||||||||||||| || |||
cctcgtggttatcaatttgctgaccccgcatcattttcta--taatgttcatttgtcagaatt-tccttaatgttaaacttgtgttta-taccttttgtatcagGTTAGATGACCCGCTTATGTGGGGATTCAAGGGTTTTCCAACTTCGGATGCAAAGCTTGGAAGGTGGGTGCTGACAGCAGAAGATATATGCTTCAAGAAT
















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|110429814|gb|EC996321.1|EC996321
EST:     TCGCGACCTCCTGGAATTCCTCTCATCACTGTTAGCAATCACATGTCGAC                         GTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGC
genomic: TCGCGACCTCCTGGCATTCCTCTCATCACTGTTAGCAATCACATGTCGACgtcagtcact ... gttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGC
EST: gi|71860869|gb|DT009924.1|DT009924
EST:     TCGCGACCTCCTGGCATTCCTCTCATCACTGTTAGCAATCACATGTCGAC                         GTTGGACGACCCAGTCGTGTGGGGATTCAAGGGTTTTCCCTCAATGGATGC
genomic: TCGCGACCTCCTGGCATTCCTCTCATCACTGTTAGCAATCACATGTCGACgtcagtcact ... gttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGC
EST: gi|71861544|gb|DT010599.1|DT010599
EST:     TCGCGACCTCCTGGCATTCCTCTCATCACTGTTAGCAATCACATGTCGAC                         GTTGGACGACCCAGTCGTGTGGGGATTCAAGGGTTTTCCCTCAATGGATGC
genomic: TCGCGACCTCCTGGCATTCCTCTCATCACTGTTAGCAATCACATGTCGACgtcagtcact ... gttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGC
EST: gi|71861757|gb|DT010812.1|DT010812
EST:     TCGCGACCTCCTGGCATTCCTCTCATCACTGTTAGCAATCACATGTCGAC                         GTTGGACGACCCAGTCGTGTGGGGATTCAAGGGTTTTCCCTCAAT
genomic: TCGCGACCTCCTGGCATTCCTCTCATCACTGTTAGCAATCACATGTCGACgtcagtcact ... gttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatggtttggataattctttactaggtcctcacatataatttctgttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGCAAAGTTGGCACGGTGGGTACTAGCAGCTGAAGATATATGCTTTAAAAAT
                           tcctcac  putative branch site (score: 2)
                                        tttctgtt  putative PPT
                                  atataatttctgttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatttctagtactaaagaagataccaataactgcttctcattcaatggtttggataattctttactaggtcctcacatataatttctgttataacagGTTGGACGACCCAGTCATGTGGGGATTCAAGGGTTTTCCCTCAATGGATGCAAAGTTGGCACGGTGGGTACTAGCAGCTGAAGATATATGCTTTAAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - -taaagaa
- - - - - - - - - - - -ataccaa
- - - - - - - - - - - - - - - - -ctgcttc
- - - - - - - - - - - - - - - - - - - - -cattcaa
- - - - - - - - - - - - - - - - - - - - - - - - -ggtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcaca