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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacagctataaccttgtgttggggttgggataatgaaaaattgctgtttgttgatttctaaccatttggtcgttaattactactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT

Basic information

species Oryza sativa
transcript LOC_Os11g43970.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------gtgacagctataaccttgtgttgg-ggttgggataatgaaaaattgctgtttgttgatttctaaccatttggtcgttaattactactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT
                                                                                            |  ||| |||   |||| | |  || |||||  || ||  || |||| |  | | |   ||  |||       ||| | | |  |  ||||||||||| ||||| || || ||||| || ||||| || ||||| |||||||| |||||||| |||||| |||   | | | |||||||||| || |||
gtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaatcgttgcttttgggtagcaatagttttgtttggttgggtgggactatcaa--atcgctgctgctggttccatattcatcaccatcttactcattgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAACAGAGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------------------gtgacagctataaccttgtgttgg-ggttgggataatgaaaaattgctgtttgttgatttctaaccatttggtcgttaattactactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT
                                                                                            |  ||| |||   | || | |  || |||||  || ||  || |||| |  | | |   ||  |||       ||| | | |  |  ||||||||||| ||||| ||||| ||||| || ||||| || ||||| |||||||| |||||||| |||||| |||   | | | |||||||||| || |||
gtaaatgttgtttcattcagtgggactggattacccagttgcataactgtagttttgttctgtgggccatggttatctaattgttgcttttgggtagcaatagtttcgtttggttgggtgggactatcaa--atcgctgctgctggttccatattcatcaccatcttactcattgtttcagGTTAATGGTAAACTTGCCTGATGCATCAAACAGAGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 15
--------gtgacagctataaccttgtgttggggttgggataatgaaaaattgctgttt--gttgatttc-taaccatttggtcgttaattactactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT
          ||   |  | ||   |  || ||       | |||       ||    |  |  |||||  | |||||||  |   | | || || |  ||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| |||||||| |||||| |||   | | | ||||| | || || |||
tgggcctttagatctcctttactagggcttaggacctacctgatgtggtgaggcaacataggcggatttaatcaccatttt-ttacttactattatttcagGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCGGATGTTGATCTCGACTCACTT

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 9
----------------------------------------gtgacagctataaccttgt--gttggggttgggataatgaaaaattgctgtttg-----------ttgatttc-taaccatttggtcgttaattactactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT
                                        || | | || ||   ||||  | ||||    |  ||   ||   ||||| || |           ||| || | ||  |||       ||| | | |  |  ||||||||||| ||||| || || ||||| ||||| || || ||||| |||||||| |||||||| |||||| |||   | | | |||||||||| || |||
gtaaatgttgtttcattcagtgggactggattacccagttgt-ataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT

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|55409323|gb|CV721699.1|CV721699
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|58691499|gb|CK080186.1|CK080186
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|8860068|gb|AU097386.1|AU097386
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGA-GTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|58607816|gb|CK035849.1|CK035849
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|218497816|gb|FG965087.1|FG965087
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|11171080|gb|AU163614.1|AU163614
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGA-GTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|29682150|gb|CB678425.1|CB678425
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|66922707|gb|CX109555.1|CX109555
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCCTTGGAACGCATCGAATAGAGAAAAGATTCCTG
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACC-T-G-A-CGCATCGAATAGAGAAAAGATTC-TG
EST: gi|15857794|gb|BI810606.1|BI810606
EST:     TCATTAGGA-GTTCCCGCCCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: TCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|8860101|gb|AU097419.1|AU097419
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGA-GTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|27554453|gb|CA998353.1|CA998353
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTACGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|58686681|gb|CK075368.1|CK075368
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
EST: gi|86831749|gb|CI301599.1|CI301599
EST:     AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAG                         GTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT
genomic: AATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGT

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: 71 (upstream exon), 71 (downstream exon)
Score: 60

ATGGATTACGCACTAAAGATAAAGAACGTGTACTGGTTCTTGGTGCCACAAATAGGCCTTTCGACCTGGATGAGGCTGTCATTAGGAGGTTCCCGCGCAGgtgacagcta ... actactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaaattgctgtttgttgatttctaaccatttggtcgttaattactactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT
                                       ttaattacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacagctataaccttgtgttggggttgggataatgaaaaattgctgtttgttgatttctaaccatttggtcgttaattactactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA