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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG

Basic information

species Oryza sativa
transcript LOC_Os11g37890.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G138907_T01 (Zea mays), 3'ss of exon 2
----aaccctagaattcct-caaaacagagc---atttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
     ||   | || | ||   | |   |||     ||| ||||     | | || ||    ||  |   | ||   |    ||||  ||  ||    | | | | |||||||| ||||| |||||||| || ||||||||||| || ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||
tggccacatgaaaactgctgtcagatgcagctgaggttaatttagagcccatctcttg----caaaaaaaaaaaagtttgaaatttctgtcgtt----tacatggcagGTTCTTCTATGCATCAAGTGCCTGCATCTACCCTGAGTTCAAGCAGCTGGAAACTGTAGTTAGCTTGAAGGAGTCCGATGCTTGGCCTGCCGAG

upper sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0030g02180.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------aaccctagaatt--cctcaaa-acagagcatttactt------------taacaatcctgtcatgttatcatcactcagaagaatcatcatt--ttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                                                    |    | ||||    |||   ||  ||||||||  |            |||   | ||      || |  |    | ||  | ||   | |   || |||||     |  | | |||||||| ||||| || |||||||| ||||||||||||||||||||| |||| |||   || |||||||||||||| ||||| ||||||||||||
gtttgttgtcttcaatttgttctatcctggctttgactaagttctccatttgatatgaaaattggtttcatgtactcagcatttatctgtctaggagacgtaaatttactaatgaatttttctggtcctgagaattctctaatatctgattattccacattgt-gcagGTTCTTCTATGCCTCTAGTGCTTGCATCTACCCTGAATTTAAGCAGTTGGAAACTAATGTGAGCTTGAAGGAGTCTGATGCATGGCCTGCAGAG

upper sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0020g04510.t01 (Vitis vinifera), 3'ss of exon 2
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaat--catcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
    ||  |   |    | |||    || || | || ||  | |  ||| |   |||  || | |  |||    ||| | ||  |  |  | |   || |||||| || ||||| || || |||||||| || ||||||||||| ||| |||| |||   || |||||||||||||| |||||||||||||| |||
gtttctttaggccactgatacatgatatataatata-cacacata-catctacccatttctgatattaatgttttcaatgtgtgtgctcgtgtgttttttagGTTTTTCTATGCATCCAGCGCTTGTATTTATCCTGAATTTAAACAGTTGGAAACTAATGTGAGCTTGAAGGAGTCTGATGCTTGGCCTGCTGAG

upper sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S171_56V6.2 (Physcomitrella patens), 3'ss of exon 1
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttatttttttt--ccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGT---TAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
     || ||| | ||       | |  |       | | | ||  | | | |  |||  |  |     ||      |  ||    ||  |     ||| ||||| || ||||||||||| || |||||||| |||||||| || |||||||| ||||  ||    ||| |||||||||| || |||||||| ||   |
gtgagtacaat-cttcttcctttaccgatcgtagagagattgctcccgtttcaa-atcttttggttttgtcggttcctgagtggagttggtggatgttgcagGTTTTTCTATGCTTCAAGCGCGTGTATCTATCCTGAATTCAAACAGCTGGAGACTGACGTGAGCAGCCTGAAGGAGTCGGACGCTTGGCCCGCTCTG

upper sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 1
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                                 |   |  |  |||       |  |   ||  ||| ||    |  |   |   ||| ||  |||  || || |||||||| || ||||| || || ||||| || |||||||||||||| |||   || || ||||||||||||||||| ||||| ||||||
--------------------------------gtagcctgtggtgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

upper sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 1
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                                 |   |  |  |||       |  |   ||  ||| ||    |  |   |   |   ||  |||  || || |||||||| || ||||| || || ||||| || |||||||||||||| |||   || || ||||||||||||||||| ||||| ||||| 
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctcgcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCAGCAGAA

upper sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ10353 (Selaginella moellendorffii), 3'ss of exon 1
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                                 |   |  |  |||       |  |   ||  ||| ||    |  |   |   | | ||  |||  || || |||||||| || ||||| || || ||||| || |||||||||||||| |||   || || ||||||||||||||||| ||||| ||||||
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctctcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

upper sequence: LOC_Os11g37890.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 1
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                                 |   |  |  |||       |  |   ||  ||| ||    |  |   |   ||| ||  |||  || || |||||||| || ||||| || || ||||| || |||||||||||||| |||   || || ||||||||||||||||| ||||| ||||||
--------------------------------gtagcctgtgatgtttctaagttgttcttcccaaggatttggagctcactctctttcttggcttccagATTTTTTTATGCGTCCAGTGCATGCATTTACCCCGAGTTTAAGCAGCTGGAGACTAACGTGAGTTTGAAGGAGTCAGATGCATGGCCGGCAGAG

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|88430768|gb|CI596882.1|CI596882
EST:     ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAG                         GTTCTTTTATGCTTCAAGTGCTTGTATC
genomic: ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgtaacttttg ... ttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATC
EST: gi|29614322|gb|CB619335.1|CB619335
EST:     ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAG                         GTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
genomic: ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgtaacttttg ... ttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
EST: gi|29661000|gb|CB657275.1|CB657275
EST:     ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAG                         GTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
genomic: ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgtaacttttg ... ttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
EST: gi|29682074|gb|CB678349.1|CB678349
EST:     ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAG                         GTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
genomic: ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgtaacttttg ... ttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
EST: gi|55828196|gb|AU067845.2|AU067845
EST:     ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAG                         GNTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCT
genomic: ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgtaacttttg ... ttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCT
EST: gi|29642083|gb|CB647090.1|CB647090
EST:     ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAG                         GTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
genomic: ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgtaacttttg ... ttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
EST: gi|86891813|gb|CI310031.1|CI310031
EST:     ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAG                         GTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTG
genomic: ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgtaacttttg ... ttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTG
EST: gi|58592572|gb|CF990880.1|CF990880
EST:     ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAG                         GTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA
genomic: ATGATCAGCTTTAACATGCTTGAGGCCGCTAGGATTAATGGTGTCAAAAGgtaacttttg ... ttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG
                              ttttggttattttttt  CT-rich tract
                          atcattttggttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaccctagaattcctcaaaacagagcatttactttaacaatcctgtcatgttatcatcactcagaagaatcatcattttggttattttttttccttgtagGTTCTTTTATGCTTCAAGTGCTTGTATCTACCCTGAATTTAAGCAGCTGGACACTGTAGTTAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG