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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcgattcctcaaattatttatgttttcctgtgttctccgtatggtcccattaacagcatttcatgttgaggatttctgcagcatacagtaca...

Basic information

species Oryza sativa
transcript LOC_Os01g46980.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G070360_T01 (Zea mays), 5'ss of exon 2
AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcgattcctcaaattatttatgttttcctgtgttctccgtatggtcccattaacagcatttcatgttgaggatttctgcagcatacagtaca--
| ||||| ||||||||||| || |||||||||||||||||||||||||| || ||||| |||||||| ||||||||||| || |||||  | |||||||||| ||||||| ||||    ||||  ||    | | |  |   |   |||    ||    || |  || || |    | ||  |      | |   |   |  
AATTCAACATTGAGAAGCTGCAGCTTGTTGAAGCTGAGAAAAAGAAGATTAGACAAGAGTATGAACGCAAAGAGAAGCAGGTTGAAGTACGGAAGAAAATgtaagacttcaattctatgaatttgttcacctcttcgataaaca--gtaattgccatggaatatgatgtcgttgccatgaaatgcatttcgtgttgagaatg

upper sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G030167_T01 (Zea mays), 5'ss of exon 2
AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcgattcctcaaattatttatgttttcctgtgttctccgtatggtcccattaacagcatttcatgttgaggattt--ctgcagcatacagtaca---
| ||||| ||||||||| | || ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| || |||||  | |||||||||| ||||||| ||||  | ||||      |||  |||      |   ||     |  |||   ||  |  |   ||| | | |  |      || || | ||   
AATTCAACATTGAGAAGTTGCAGCTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAGTATGAACGCAAAGAGAAGCAGGTTGAAGTACGCAAGAAAATgtaagacttcaattctccgaatt-----cgttcacctcaaggataaatagtagtctgttagttgctatcaaatatgatgttcttgccatgaaatgcatttcatgt

upper sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G02390.3 (Glycine max), 5'ss of exon 2
AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcgattcctcaaattatttatgttttcctgtgttctccgtatggtcccattaacagc-atttcatgttgaggatttctgcagcatacagtaca----
| |||||||| |||||||| ||  | |||||||| || || |||||||||||||||||||| ||||| ||||||   ||||||||| || | ||||| ||||   |||||      |  || | | |||  | |  | | || ||  | ||    |  ||  | | |  |||| | |    ||      |  || | |  |    
AATTCAATATCGAGAAGCTGCAGTTGGTTGAAGCCGAAAAGAAGAAGATCAGGCAAGAATACGAACGCAAAGAGCGCCAAGTCGAAATTCGCAAGAAGATgta--acttc---ctatataactctctatcctctttttttttgtctctgtgagttcgatattaactaggtcatctcgtccgttgacatcgattaaaattaaattc

upper sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G37160.1 (Glycine max), 5'ss of exon 2
AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcg-attcctcaaattatttatgttttcctgtgttctccgtatggtcccattaa--cagcatttcatgtt-gaggatttctgcagcatacagtaca
| |||||||| |||||||| ||  | || ||||| || || |||||||||||||||||||| ||||| ||||||   ||||||||| || | ||||| |||| |        ||  |||    || |  | | ||  | ||||    ||  | ||  | | |   ||   |||  ||  |  ||| || |  | |   |     
AATTCAATATCGAGAAGCTGCAGTTGGTCGAAGCCGACAAGAAGAAGATCAGGCAAGAATACGAACGCAAAGAGCGCCAAGTCGAAATTCGCAAGAAGATgtaacttcctacataactctctatactcctttgtttttttgtttcttgtgagttcgaaattagttaggtcttctcgtccgttgatatcagttgaaattaa----

upper sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G37190.1 (Glycine max), 5'ss of exon 2
AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcgattcctcaaattatttatgttttcctgtgttctccgtatggtcccattaacagcatttcat--gttgaggatttctgcagcatacagtaca--
| |||||||| |||||||| ||  | || ||||| || || |||||||||||||||||||| ||||| ||||||   ||||| ||| || | ||||| |||| |  ||||  | | | |   | | ||   |||  |    |||  ||  |     | | |   | | || |  |||||       || |   || | |     
AATTCAATATCGAGAAGCTGCAGTTGGTCGAAGCCGACAAGAAGAAGATCAGGCAAGAATACGAACGCAAAGAGCGCCAAGTTGAAATTCGCAAGAAGATgtaa--cttcc-tacataactctctatactctttttttgtctctgagttcgaaattagttaggtcttctcgtccgttgacatcggttgaaat-taaattctgga

upper sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G37150.1 (Glycine max), 5'ss of exon 2
AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcgattcctcaaattatttatgttttcctgtgttctccgtatggtcccattaa--cagcatttcatgtt-gaggatttctgcagca-tacagtaca
| |||||||| |||||||| ||  | || ||||| || || |||||||||||||||||||| ||||| ||||||   ||||| ||| || | ||||| |||| |  ||||  ||  | |   | |  |  ||||  | |||     |   | ||  | |||   ||   |||  ||  |   || || |  | | |  | | | 
AATTCAATATCGAGAAGCTGCAGTTGGTCGAAGCCGACAAGAAGAAGATCAGGCAAGAATACGAACGCAAAGAGCGCCAAGTTGAAATTCGCAAGAAGATgtaa--cttcc-tttataactctctacacttttttttttgtctcttgcgagttcgaaataagttaggtcttctcgtccgttaatatcagttgaaattaaattc-

upper sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv02s0025g01000.t01 (Vitis vinifera), 5'ss of exon 2
AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcgattcctcaaattatttatgttttcctgtgttctccgtatggtcccattaacagcattt-catgttgaggatttctgcagcatacagtaca-----
| ||||| ||||||||| | || ||||||||||| ||||| ||||||||||| || |||||||| || |||||||||||||| ||  || | |||||||||| |      ||    |     || ||   || |   |  || |  ||  | || ||||   || |||    |||||   |  |||     ||  | | |      
AATTCAACATTGAGAAGTTGCAGCTTGTTGAAGCGGAGAAGAAGAAGATCAGACAGGAATATGAGCGAAAAGAGAAGCAAGTTGATATTCGGAAGAAAATgtaaattactgaactatg----tacttgatttctttggcatttttggt--gatcacattgtgagaattggtttgttgttaagctctaagctatggatttctgatca

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|33800263|gb|CF325997.1|CF325997
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|40486588|gb|BX898040.1|BX898040
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTAAGCAACTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|56550159|gb|CX056263.1|CX056263
EST:     AAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|58593493|gb|CF991801.1|CF991801
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAACTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|29639860|gb|CB644869.1|CB644869
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|218488190|gb|FG970074.1|FG970074
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAACTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|58604131|gb|CK014659.1|CK014659
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAACTGAATGGTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|58586214|gb|CF984522.1|CF984522
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAACTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|55411972|gb|CV724348.1|CV724348
EST:     AGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|58594166|gb|CF992474.1|CF992474
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAACTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|88392356|gb|CI612830.1|CI612830
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
EST: gi|2310524|gb|C26679.1|C26679
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAGCTGAATGCTTTCTCGCATCAAAGTGCTTCAAGCTC
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTT-CTCGCATCAAAGTGCTTCAAGCTC
EST: gi|33657536|gb|CF280150.1|CF280150
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTT
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTT
EST: gi|33688006|gb|CF316245.1|CF316245
EST:     AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAAT                         TGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA
genomic: AGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCA

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: 74 (upstream exon), 73 (downstream exon)
Score: 144

AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttc ... cctttatcagTGAGTACTCTATGCAGCTGAATGCTTCTCGCATCAAAGTGCTTCAAGCTCAGGATGATTTGGTTAATTCCATGAAAGAGGATGCTACAAAGCAACTCCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTCAATATTGAGAAGCTTCAACTTGTTGAAGCTGAGAAAAAGAAGATCAGGCAAGAATATGAACGGAAAGAGAAGCAAGTCGAAGTTAGAAAGAAAATgtgagacttcgattcctcaaattatttatgttttcctgtgttctccgtatggtcccattaacagcatttcatgttgaggatttctgcagcatacagtaca

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA