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

gtaagttatcctacttcattcccttggttgaacagatgagcttcccctttttcatgtgtggtaaactatcataagttgtacgtttgttgtttactgttttgttagtgttagttgacttaagatttcaagggttatatgcaacttattgcgtctttaaacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG

Basic information

species Oryza sativa
transcript LOC_Os07g48300.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G030646_T02 (Zea mays), 3'ss of exon 6
gtaagttatcctacttcattcccttggttgaacagatgagcttcccctttttcatgtgtggtaaactatcataagttgtacgtttgttgtttactgttttgttagtgttagt-tgacttaagatttcaagggttatat------gcaacttattgcgtctttaaacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG
||||| |||||   || ||| | ||| |        |  || |       |  ||| ||| |    |    | |   | |   ||| ||||| || || || | |  | | | ||| |  || || |     || | |      || |  |    | |   | ||  |  |||||||||| ||||| |||||||| ||||| ||||||||||| ||| | ||||| |||||||||||||||||||||||||||||||||
gtaagctatccattttgattgcgttgatatttgtagtatgcctttttggatatatg-gtgctgctttccttttataagcatacttgctgtttgctattatgattgaataaatatgattgtagtttaccttttttctctctccccgcgatctgaaacttgactgaatttcacagATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG

upper sequence: LOC_Os07g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G080048_T01 (Zea mays), 3'ss of exon 7
gtaagttatcctacttcattcccttggttgaacagatgagcttcccctttttcatgtgtggtaaactatcataagttgtacgtttgttgtttactgttttgttagtgttagttgacttaagatttcaagggttatatgcaacttattgcgtctttaa--acctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG
||||||||||| | || ||  | ||| |        |  ||||    |||||       | | |  | | ||||| |      ||| ||||| ||| | || | |  | | |    |     |||   |  ||     |  ||   ||    || |   |  | ||||||||||||||||| |||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
gtaagttatccaatttgatcgcgttgatacttgtagtatgcttttttttttttgaaca-gatga--tgttataagcta----cttgctgtttgctgatatgattgaataaatatgatggttgtttattgtttttctccctgctatctgaaagttgactcatttctcagATGAGTACGTCATCTGCAATGGATGCAAGAGCCCTGATACCATTCTGTCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG

upper sequence: LOC_Os07g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagttatcctacttcattcccttggttgaacagatgagcttcccctttttcatgtgtggtaaactatcataagttgtacgtttgttgtttactgttttgttagtgttagttgacttaagatttcaagggttatatgcaactta-ttgcgtctttaaacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG
                                                                    |  ||  |  || || ||  | |  | ||||| || || |   || |  | | |    |  ||  |  |    |||| ||||  ||       || |||| ||||||||||| |||||||||||||| ||||||||||||||||| |||||||| ||||| |||||||||||||| || ||||||
------------------------------------------------------------------atttttacctcctaagtatga-gatcgcagttttttttgtatacctttatctgaaaaggaagtggaaaggttattcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG

upper sequence: LOC_Os07g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------gtaagttatcctacttcattcccttggttga-acagatgagcttcccctttttcatg---tgtggtaaactatcataagttgtacgtttgttgt-ttactgttttgttagtgttagttgactt--aagatttcaagggttatatgcaacttattgcgtctttaaacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG
                            |  ||  | |||   || |   |  |  |   ||        || | |    || |   |     |  | ||||||    ||     ||  |  ||| | || ||||      | |   ||   |||   | || |  | |||   || | |  | || ||  |  || |||||||||| || || |||||||||||||| || || || || || || |||||||| ||||| |||||||| ||||| || ||||||
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgt-acttcatt--atgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG

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|33824940|gb|CF338274.1|CF338274
EST:     AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
EST: gi|89163018|gb|CI099908.1|CI099908
EST:     AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
EST: gi|33658199|gb|CF280813.1|CF280813
EST:     CGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: CGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
EST: gi|25803992|gb|CA759953.1|CA759953
EST:     AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
EST: gi|55409065|gb|CV721441.1|CV721441
EST:     AGGAAGATTTGCTCCGAAAAACTTCGAAACAATCCTGCGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
EST: gi|88990737|gb|CI108124.1|CI108124
EST:     AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
EST: gi|88238682|gb|CI238531.1|CI238531
EST:     AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
EST: gi|38481420|gb|CF965509.1|CF965509
EST:     AGGAAGATGTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
EST: gi|66923189|gb|CX110037.1|CX110037
EST:     AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCA                         ATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA
genomic: AGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCA

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: 66 (upstream exon), 44 (downstream exon)
Score: 17

GAAATGGGGACAAGTGGATCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGATTTGCTCCGAAAAACTTCGAAGCAATCCTGCGGAGATATATCAgtaagttatc ... aacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacttaagatttcaagggttatatgcaacttattgcgtctttaaacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG
 agttgac  putative branch site (score: 17)
                                               cctttc  putative PPT
     ttaagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatcctacttcattcccttggttgaacagatgagcttcccctttttcatgtgtggtaaactatcataagttgtacgtttgttgtttactgttttgttagtgttagttgacttaagatttcaagggttatatgcaacttattgcgtctttaaacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA