Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatacatctctctgtctttctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG

Basic information

species Vitis vinifera
transcript Vv13s0067g00220.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 3'ss of exon 1
gtaagctatacatctctctgtctttctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgcctt-tgtcggtgtgggtgatgtattattttg---aatgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
| || | || | | | ||| | | | | | || | || || ||| || || || | || | ||| ||| |||| || | | |||| || || || ||||||||||||| || ||||||||||| ||| |||||||||||||||| || || ||||||||||||||||| ||||||| || |
-------------------------------gttagtat---accaactactactgcagtaaagattcagagatggaagtattt--ttactgttttctgagtgattgatttttgttttaatttgcgcgatcttccacagATCCTTGCCCCACTGCCAATCGGGTTTGCGGTGTTCTTGGTTCACCTGGCCACCATCCCCATCACCGGCACCGGCATCAACCCAGCGAGGAGCCTTGGCG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g44630.2 (Oryza sativa), 3'ss of exon 3
gtaagctatacatctctctgtctttctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaa-agATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
| | ||| | || | | | | | ||| | | ||| || | |||| | || | ||| | | ||| ||| || |||| || || || ||||||| || || || |||||| |||| ||| |||||||||||||||| || || || |||||||||||||| ||||||| || |
--------------------------tttgctcaagaaattgactgt-atgcgtatagttactggaagtatatatgggttttttgtgtgttgcat-----aacgtatttc-tgtcctttgttg---gtgaaaacagATCCTTGCCCCACTGCCAATTGGTTTTGCGGTGTTCCTGGTCCACCTGGCCACCATCCCCATCACCGGTACTGGCATCAACCCAGCCAGGAGCCTTGGCG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 2
gtaagctatacatctctctgtctttctctttctcagactctcacga-tcacccactcaatcactcactttgtcatcaagttaattaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaa-agATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
| || | | | | || | ||| | | || || | | ||||| || | | ||| | || ||| || |||| || || || ||||||| |||||||| |||||| |||| ||| | |||||||||||||| ||||| || ||||||||||||||| ||||||| || |
----------------------------------gtgtttcaacaaattgaaaatgtatgcatactcttcgata-catatttttca--tattgtgttaagacttacgatgaatgaaacccttatttggtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G392975_T03 (Zea mays), 3'ss of exon 2
gtaagctatacatctctctgtctttctctttctcagactctcacgat-cacccactcaatcactcactttgtcatcaagtta-attaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaa-agATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
| | | | | | |||| | || | || ||| || ||||| || || ||| || || |||| ||||| ||| || |||| || || || ||||||| |||||||| |||||| |||| ||| | |||||||||||||| || || |||||||||||||| ||| ||||||| || |
-------------------------------aacgaattgaaaatacatgcatactcttcaatacatgtcgttttcatattgtattaagacttacc---gtcaatgaaacccat-tatttttttg---gtgaaaacagATCCTTGCCCCACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G174807_T01 (Zea mays), 3'ss of exon 2
gtaagctatacatctctctgtctttctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaa-agATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
| | | | ||| | || | | | || | | ||| || | | | | ||| ||| || || | || || | | | || |||| || || || | ||||||||||| || |||||| | || ||| ||||||||||||| || || || |||||||||||||| || |||||||| || |
----------------------------gtgagtacagtatcagccttgccttcctgcttattcgcctcgtcc----gtccgtgcaagctcgactt-atcgatg--------gtttctttgtggacgaatgaacagATCCTCGCCCCTCTTCCAATCGGGTTTGCCGTGTTCCTCGTCCACCTGGCCACCATCCCTATCACCGGCACCGGCATCAACCCCGCGCGGAGCCTTGGCG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S1_535V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaagctatacatctctctgtctttctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgccttt-gtcggtgtgggtgatgtattattttgaatgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
|| || |||| ||| || | | ||| ||| ||| | || || | ||| || || | | | || | ||| | | | || || | || || | || || || | || ||||| |||||||| ||| ||||||||||||||||||| ||||| || ||||| ||||||||||| || || || || ||||
gtgag---taca---ctccgtttccggtgcagttcagttct--agattaccgcgcctgagacgtgctggctgatc---tttggtactcctcacagttagatggtctcaaaatgatgct-cttcgatggacttgcagGTGCTTGCGCCTCTTCCCATCGGATTCGCAGTTTTCCTGGTGCACTTGGCCACCATTCCCATCACCGGAACTGGCATCAACCCCGCCCGTAGTCTAGGTG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S305_12V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagctatacatctctctgtctttctctttctcagactctcacgatc-acccactcaatcactcactttgtcatcaagttaattaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
||||| | | | | | | | || | ||| || |||| | ||| | || | | ||| | | | | | | || | ||||||| | || ||||| || ||||||||| ||||||||||||||||||| ||||| ||||| || |||||||||||||||| || || || |
-------------------------------ggaagactgtggctagctaagtatcgtaacaatatctt--acagcaaggctttgaatgactgag--aaacataatctctgac-caccgtctgttgtttcgtgcagTTGTTGGCACCTCTTCCCATCGGATTTGCAGTGTTCCTGGTGCACTTGGCCACCATTCCCATCACTGGTACAAGCATCAACCCAGCTCGCAGTCTCGGCG

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ18960 (Selaginella moellendorffii), 3'ss of exon 2
---------------------------------------------gtaagctatacatctctctgtctt-tctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgccttt---gtcggtgtgggtgatgtatta-----------ttttgaatgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
||| | | | | ||| |||| ||| || | | | || | | | | || || || || ||| | | ||| | | | | | |||| | ||| | | || || | |||| || | ||||||||||| || |||||| | || ||| | ||||| |||||||| ||||| || |||||||||||||| || || || ||
gtacgtttcttcttccatccaaagctttggttgattcccctctcatgaagttttgcttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacagCTTTTGGCTCCACTTCCAATCGGGTTTGCGGTGTTCCTCGTCCACCTTGCCACGATCCCCATCACTGGCACGGGCATCAACCCAGCGCGAAGTCTCGGCT

upper sequence: Vv13s0067g00220.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ11572 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------------------gtaagctatacatctctctgtctt-tctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgccttt---gtcggtgtgggtgatgtatta-----------ttttgaatgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
||| | ||| | ||| |||| ||| || | | | || | | | | || || || || ||| | | ||| | | | | | |||| | ||| | | || || | |||| || | ||||||||||| || |||||| | || ||| | ||||| |||||||| ||||| || |||||||||||||| || || || ||
gtacgtttctccttccatccaaagctttggttgattcccccctctcatgaagttttacttttcttcttcttatcttcttgtgtggttttcctagtttttcttgctgtacttcctcttatcttctccttatctcttctcctcctcatggatagatttaagatatgttccaagctcacaaactttggcgatttctacagCTTTTGGCTCCACTTCCAATCGGGTTTGCGGTGTTCCTCGTCCACCTTGCCACGATCCCCATCACTGGCACGGGCATCAACCCAGCGCGAAGTCTCGGCT

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|351019993|gb|FQ439810.1|FQ439810
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGGTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161712606|gb|FC062208.1|FC062208
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCA-TCGGGTTCGCAGTGTTCT
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCT
EST: gi|161713281|gb|FC063083.1|FC063083
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGC-AATCGGGTTCGCAGTGT-CTTGGT
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGT
EST: gi|110689996|gb|EE066710.1|EE066710
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161714519|gb|FC062969.1|FC062969
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTG-CC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161713584|gb|FC063407.1|FC063407
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAA
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAA
EST: gi|161716221|gb|FC069499.1|FC069499
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCCATCGGGTTCGCAGTGTTCT
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCT
EST: gi|33409723|gb|CF215350.1|CF215350
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161720336|gb|FC071189.1|FC071189
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161719835|gb|FC065771.1|FC065771
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|33409719|gb|CF215346.1|CF215346
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161713560|gb|FC062505.1|FC062505
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGC
EST: gi|161719932|gb|FC066129.1|FC066129
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCA
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCA
EST: gi|161713874|gb|FC062564.1|FC062564
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161715641|gb|FC067783.1|FC067783
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACT
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACT
EST: gi|33409074|gb|CF214701.1|CF214701
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161717612|gb|FC065625.1|FC065625
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|161712029|gb|FC060045.1|FC060045
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
EST: gi|110732652|gb|EE108136.1|EE108136
EST:     TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCT                         ATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC
genomic: TCTTCTCCGCCACTGACGCCAAGCGTAACGCTAGAGACTCCCACGTCCCTgtaagctata ... tgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG
 aattaat  putative branch site (score: 3)
 tattattttgaatgtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctatacatctctctgtctttctctttctcagactctcacgatcacccactcaatcactcactttgtcatcaagttaattaattattgcctttgtcggtgtgggtgatgtattattttgaatgtgttaaagATACTGGCACCGTTGCCAATCGGGTTCGCAGTGTTCTTGGTGCACTTGGCCACCATCCCCATAACTGGAACCGGCATCAACCCAGCTCGGAGCCTGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC