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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcgaattcttgatccttgcaagccttgcaatatatgaattaggggcaattttggggattttaataatccatggtaatggtgctcacaatctcacctgctactgttatacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG

Basic information

species Oryza sativa
transcript LOC_Os01g67850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67850.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G058450_T02 (Zea mays), 3'ss of exon 2
gtatatcgaattcttgatccttgcaagccttgcaatatatgaattaggggcaattttggggat-tttaataatccatggtaatggtgctcacaatctcacctgctactgttatacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG---------------------------------
   || |||    | |  | |  | ||    |   |   |||||    | | |  |    | | | |  | |  | | | |||| ||  |||  |||           |||  ||   ||||| ||||| ||||| |||||||| ||||||||||   | |||||||| || ||||| |||||||||||                                   
--gtaccgacgaatagcacttgccgaga---gagtttgctgaatccacgacgaactgactggtatctcctgaggctttg-aatgttga-cacggtcttg------gtggttgaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCA---TAGAAAGGAGGGCGAGCCTGAAGGAATTCTACAGTATGCTTACTATCCACCATAGAAACTAGTGAT

upper sequence: LOC_Os01g67850.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G058450_T01 (Zea mays), 3'ss of exon 2
gtatatcgaattcttgatccttgcaagccttgcaatatatgaattaggggcaattttggggat-tttaataatccatggtaatggtgctcacaatctcacctgctactgttatacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG
   || |||    | |  | |  | ||    |   |   |||||    | | |  |    | | | |  | |  | | | |||| ||  |||  |||           |||  ||   ||||| ||||| ||||| |||||||| ||||||||||   | |||||||| || ||||| |||||||||||  
--gtaccgacgaatagcacttgccgaga---gagtttgctgaatccacgacgaactgactggtatctcctgaggctttg-aatgttga-cacggtcttg------gtggttgaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCA---TAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA
















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|33677048|gb|CF305287.1|CF305287
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|41884252|gb|BX929083.1|BX929083
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|88741864|gb|CI764369.1|CI764369
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|33693004|gb|CF321243.1|CF321243
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGGTGAGGATGCCTCTATATCCACCAATATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|33654303|gb|CF276917.1|CF276917
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|88391425|gb|CI598243.1|CI598243
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|88349124|gb|CI678094.1|CI678094
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|88442752|gb|CI693758.1|CI693758
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|88588287|gb|CI706094.1|CI706094
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|88762905|gb|CI772461.1|CI772461
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|88740582|gb|CI764090.1|CI764090
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|55410340|gb|CV722716.1|CV722716
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|66920252|gb|CX107100.1|CX107100
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|33688529|gb|CF316768.1|CF316768
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|33680394|gb|CF308633.1|CF308633
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|8857824|gb|AU095142.1|AU095142
EST:     ATACCCTCCCTAAGTTACCTAAGGTCTCCTTGANGGTCCTGGTGTACAAG                         GNATATGTTGATGAAGANGCCTCTATATCC
genomic: ATACCCTCCCTA-GTTACCTA-GGTCTCCTTGA-GGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCC
EST: gi|33693589|gb|CF321828.1|CF321828
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|33679207|gb|CF307446.1|CF307446
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|88851912|gb|CI679470.1|CI679470
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
EST: gi|33685055|gb|CF313294.1|CF313294
EST:     CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAG                         GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA
genomic: CATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCA

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: 52 (upstream exon), 60 (downstream exon)
Score: 28

TCCAATCATCCTTAACCTCATCCAGTGGATGGATTGCAGCTGCTCCCTTTCATATACCCTCCCTAGTTACCTAGGTCTCCTTGAGGTTCTTGTGTACAAGgtatatcgaa ... atacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataatccatggtaatggtgctcacaatctcacctgctactgttatacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG
                                              tacctcc  CT-rich tract
                                         tgttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcgaattcttgatccttgcaagccttgcaatatatgaattaggggcaattttggggattttaataatccatggtaatggtgctcacaatctcacctgctactgttatacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA