Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCTTGATCGAGAAGGAATTAGCTTTTGCTGTCGAACTACATATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgccttgttctgttataaagttcattagatgtgacctttttgaacttgcatctgtattaatactgttttatccccag

Basic information

species Oryza sativa
transcript LOC_Os02g48964.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G109039_T04 (Zea mays), 5'ss of exon 1
--------CACCTTGATCGAGAAGGAATTAGCTTTTGCTGTCGAACTACATATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgccttgttctgttataaagttcattagatgtgacctttttgaacttgcatctgtattaatactgtttt---atccccag
        ||||||||||  ||||| ||||| |||||||||||||| || |||||||| || |||||||| ||||| ||||||||||| |||||  | |||||| | ||    | |||||  ||       |||||  |||||     ||    || | |  |||| |||||||   | ||||||
AAATGCAGCACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttcccatctgtgttactaa-------agatgctaccttaccatacacatatttattctaattctgtttttgcacccccag

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G109039_T01 (Zea mays), 5'ss of exon 7
CACCTTGATCGAGAAGGAATTAGCTTTTGCTGTCGAACTACATATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgccttgttctgttataaagttcattagatgtgacctttttgaacttgcatctgtattaatactgtttt---atccccag
||||||||||  ||||| ||||| |||||||||||||| || |||||||| || |||||||| ||||| ||||||||||| |||||  | |||||| | ||    | |||||  ||       |||||  |||||     ||    || | |  |||| |||||||   | ||||||
CACCTTGATCAGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttcccatctgtgttactaa-------agatgctaccttaccatacacatatttattctaattctgtttttgcacccccag

upper sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G048045_T01 (Zea mays), 5'ss of exon 7
CACCTTGATCGAGAAGGAATTAGCTTTTGCTGTCGAACTACATATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgccttgttctgttataaagttcattagatgtgacctttttgaacttgcatctgtattaatactgtttt---atccccag
||||||||||| ||||| ||||| |||||||||||||| || |||||||| || |||||||| ||||| ||||||||||| |||||  | |||||| | |||   | |||||  ||      ||  | | ||| | |    |    ||   | ||||| |||||||   | ||||||
CACCTTGATCGGGAAGGTATTAGTTTTTGCTGTCGAACAACTTATGATGATAATGCTATTACAAATGCGGTTGAGATATTTAATACCTCTAGgtaacttcctctctgtgttactaaagatgcta--tctcaccgtat---gcacatattcattttaattctgtttttgcacccccag

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|218482014|gb|FG963446.1|FG963446
EST:     TGAAAACGCTATTACTAATGCTGTTGAGATA-NCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: TGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|29671102|gb|CB667377.1|CB667377
EST:     TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGNTA-GAGACT
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTG-TAAGAGACT
EST: gi|29677180|gb|CB673455.1|CB673455
EST:     ATGATGAAAACGCTATTACTAATGCTG-TGNAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: ATGATGAAAACGCTATTACTAATGCTGTTG-AGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|29671103|gb|CB667378.1|CB667378
EST:     AGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: AGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|163922839|gb|EG712235.1|EG712235
EST:     ACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: ACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|218482945|gb|FG948107.1|FG948107
EST:     TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTG
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTG
EST: gi|25801428|gb|CA757389.1|CA757389
EST:     TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|218501212|gb|FG955432.1|FG955432
EST:     TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|27548190|gb|CA766256.2|CA766256
EST:     TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|29619648|gb|CB624660.1|CB624660
EST:     TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|29672639|gb|CB668914.1|CB668914
EST:     ATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: ATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|218495836|gb|FG960244.1|FG960244
EST:     TATGATGAAAACGCTATTACTAATGCTG-TGAGATA-TCAATACTACCAG                         TGGTGCTGTCCACTTCATGGCATCGAATAATGACTCTGGTGT-GGAGACTA
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|29674117|gb|CB670392.1|CB670392
EST:     TATGATGAAAACGCTATTATTAATGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATAGAATAATGACTCTGGTGTAAGAGACTA
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
EST: gi|29672638|gb|CB668913.1|CB668913
EST:     TATGATGAAAACGCTATTACTAGTGCTGTTGAGATATTCAATACTACCAG                         TGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA
genomic: TATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTA

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: 58 (upstream exon), 62 (downstream exon)
Score: 27

CACCTTGATCGAGAAGGAATTAGCTTTTGCTGTCGAACTACATATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgcct ... ttatccccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCTTGATCGAGAAGGAATTAGCTTTTGCTGTCGAACTACATATGATGAAAACGCTATTACTAATGCTGTTGAGATATTCAATACTACCAGgtaattgccttgttctgttataaagttcattagatgtgacctttttgaacttgcatctgtattaatactgttttatccccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT