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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgcaatcattacatagccataacaattacgacatgtggatttatttaactttattttgttggaagccgctagttatttttcaaattttgtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCTAGCAAGCCTGGCTTGTTTGGATCTAGAATCAAGTGGAACTTTACCAAAT

Basic information

species Oryza sativa
transcript LOC_Os03g24380.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G329144_T01 (Zea mays), 3'ss of exon 4
cttgcaatcattacatagccataacaat-tacgacatgtggatttatttaactttatt--ttgttggaagccgctagttatttttcaaattttgtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCTAGCAAGCCTGGCTTGTTTGG---ATCTAGAATCAAGTGGAACTTTACCAAAT
     |  | | |||     | | |||  | | |   |  | | | | |   | ||||  |  ||  |    |||  ||   ||  ||| |  |  | |||||||||| ||||| || || ||||| || ||  ||||||| ||| ||||||||||||||||||| ||||||||   ||| || ||||| |||||||||||||   
---atagacctgacaggttgacatcaacgtgcaaaccggagctgtgtgttcttatattgctaattaaagaaagctgattgcattctaaactcgggttttgcagGTGCGCGTAAACGGACCAGATGCGGCGCCGGTTTACAAGTTTCTGAAAGCTAGCAAGCCTGGTTTGTTTGGGTCATCAAGGATCAAATGGAACTTTACCA---

upper sequence: LOC_Os03g24380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 4
cttgcaatcattacatagccataacaattacgacatgtggatttattta---actttattttgttggaagccgctagttatttttcaaattt--tgtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCTAGCAAGCCTGGCTTGTTTGGATCTAGAATCAAGTGGAACTTTACCAAAT
  ||   || |||    | |  |  |||| | |||| | | |    | |     ||||  | |||  |      |  | | | ||||| | |  | | | |  |||| ||||||||||| ||||||||||||||| | ||||||||  | |||||   |||   ||| ||  |||||||||| ||||| ||||| || ||||| |
-atgtg-tctttattgggtctca--aatttctacattttgctccgatcataggatttacatagttaaatat-aatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT
















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|30228288|gb|CB966179.1|CB966179
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|29639181|gb|CB644190.1|CB644190
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|8527832|gb|AU092647.1|AU092647
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|25807079|gb|CA763033.1|CA763033
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCCCTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|7378306|gb|AU088577.1|AU088577
EST:     AGGATTTTGCTTGCNCAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGNCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|88471220|gb|CI408491.1|CI408491
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGGT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|30227513|gb|CB965405.1|CB965405
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|8528179|gb|AU092994.1|AU092994
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|3762605|gb|AU029357.1|AU029357
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|38565824|gb|CK085277.1|CK085277
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|8528215|gb|AU093030.1|AU093030
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|29639182|gb|CB644191.1|CB644191
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
EST: gi|58587054|gb|CF985362.1|CF985362
EST:     AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAG                         GTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT
genomic: AGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCT

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: 72 (upstream exon), 69 (downstream exon)
Score: 72

TCCCTGCAATCAGTTCTTGCGACAAGAGCCAGGATCTGACCAGCAAATAAAGGATTTTGCTTGCACAAGATTTAAAGCTGAATATCCCGTTTTTCAGAAGgtaagaacta ... gtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCTAGCAAGCCTGGCTTGTTTGGATCTAGAATCAAGTGGAACTTTACCAAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactttattttgttggaagccgctagttatttttcaaattttgtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCTAGCAAGCCTGGCTTGTTTGGATCTAGAATCAAGTGGAACTTTACCAAAT
 atttaac  putative branch site (score: 72)
                          tagttatttttcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgcaatcattacatagccataacaattacgacatgtggatttatttaactttattttgttggaagccgctagttatttttcaaattttgtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCTAGCAAGCCTGGCTTGTTTGGATCTAGAATCAAGTGGAACTTTACCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
cttgcaa
- - - - - - - - - -cataacaa
- - - - - - - - - - - - - - - - -catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccgcta