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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttgctattgatctatgattttgctatatcaattttctaacagggtttataatgttcaattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC

Basic information

species Oryza sativa
transcript LOC_Os05g38550.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 3
gtaagc-ttgctattg------atctatgattttgctatatcaattttctaacagggtttataatgttcaattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC
|||||| | |||||         ||||  ||||    ||  |||  |||| |||    || |  | || |||||| ||||||||||||||| || || ||||||||||| |||||||||||||| ||||||||||| |||||||||||||| |||||||| |||||||| ||||| ||
gtaagcatcgctatcatgtcttgtctactatttgatcatgccaaagttctgacaattctttttgttttgaattctcagTTTATCCTGATGGACGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAATGGTTATGAGCTTGCAAGCGAACGATGGACACCAGTGCACAC

upper sequence: LOC_Os05g38550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
gtaagctt-gctattga------------tctatgattttgctatatcaattttctaacagggtttataatgttcaattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC
||||||||  |||| |             ||||  || |    || ||||  |||| |||    |||| || || |||||| ||||||||| |||||||| || ||||||||||| |||||||||||||| ||||||||||  |||||||||||||| ||||||||||||||||| ||||| ||
gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC

upper sequence: LOC_Os05g38550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G06960.1 (Glycine max), 3'ss of exon 3
gtaagcttgctatt--gatctatgattttgct---atatcaattttctaacag-ggtttataatgttcaattctt--agTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC
|| ||  |  | ||   || | ||||||||||   || | || |   | | || | | | |  ||||||||| ||  ||| ||||| ||||| || || ||||| || || |||||||| ||||| || ||||| || ||||| ||||||||||| || || ||||||||||| |||||
gttagtgttttttttgaatttgtgattttgctttgatttgaactacatgaaagtgatgttttctgttcaatttttgcagTATATCCCGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTACGAGCTTGCGAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: LOC_Os05g38550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
----gtaagcttgctattgatctatgattttgct---atatcaattttctaacagggttta--------taatgttcaattctt--agTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC
    ||    ||  | || || | ||||||||||   |||  ||     | | || | | |        |  ||||||||| ||  ||| ||||||||||| || || ||||| || || |||||||| ||||| || ||||| || |||||||||||||| || || || ||||||||||| |||||
gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: LOC_Os05g38550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 3
gtaagcttgctattgatctatgattttgctat-atcaattttctaacagggtttataatgttcaattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC
||  |  ||  |    | | | ||  ||||   || |||     ||      | ||  |||||||||   ||| |||||||||||||| || ||||| || || |||||||| ||||| || || || || |||||||||||||| || || || ||||| ||||| |||||
gttggtctgacacattttttttatcctgcttcgattaatacatgaaattcaatgatgttgttcaatttgcagTGTATCCTGATGGGCGAGTTTGCATATCAATTCTTCATCCTCCTGGTGACGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: LOC_Os05g38550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G59300.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------gtaagcttgctattgatctatg---attttgctatat--caattttctaacagggtttataatgttcaattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC
                      |      |  |  |||  |     || |   || |   ||    | | |  || ||  | || ||        ||||||| ||||||| || || ||||| ||||| |||||||| || || || ||||| | ||||||||||||||| ||||| || ||||| ||||| |||||
gttagttttctctctatcggttttgatcggggaaggattcaaaggaatatgaatagaagacagacgtttgaatggtttacttatatttgtcctgcagTTTATTCTGATGGTCGTGTTTGCATATCTATTCTTCATCCTCCCGGTGATGATCCTAGCGGTTATGAGCTTGCAAGCGAGCGTTGGACTCCTGTTCATAC

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|29680264|gb|CB676539.1|CB676539
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|33683398|gb|CF311637.1|CF311637
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCTAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|33653640|gb|CF276254.1|CF276254
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|3760646|gb|C97900.1|C97900
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|55827422|gb|AU030093.2|AU030093
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTTGGCGAA
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCT-GGCGAA
EST: gi|38470738|gb|CF954869.1|CF954869
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGTGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|286322|gb|D15130.1|D15130
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATN                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|86822730|gb|CI251810.1|CI251810
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCATCTGGCGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|22306772|gb|BQ907994.1|BQ907994
EST:     ATCAGTAAGGTTTACCTCTGAGATGTGGCATCC-AATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGTGAAG
genomic: ATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|33658681|gb|CF281294.1|CF281294
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|86524276|gb|CI164482.1|CI164482
EST:     GCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: GCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|33658854|gb|CF281467.1|CF281467
EST:     AGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: AGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|29616092|gb|CB621104.1|CB621104
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGTGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|29685177|gb|CB681452.1|CB681452
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
EST: gi|29688855|gb|CB685130.1|CB685130
EST:     GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATG                         TTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG
genomic: GAATAGTCCCCCATCAGTAAGGTTTACCTCTGAGATGTGGCATCCAAATGgtaagcttgc ... caattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatgattttgctatatcaattttctaacagggtttataatgttcaattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC
                       ttctaac  putative branch site (score: 1)
                                                ttctt  putative PPT
             tatatcaattttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttgctattgatctatgattttgctatatcaattttctaacagggtttataatgttcaattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA