Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaactaccttgttgacattatgtgtgaacatcactgagactgtgatcagaacttcagaattttgaaatctcaataatctaactacaatcatgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGG

Basic information

species Oryza sativa
transcript LOC_Os05g19954.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g19954.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G095782_T04 (Zea mays), 3'ss of exon 2
--ataaactac--cttgttgacattatgtgtgaacatcactgagactgtgatcagaacttcagaattttgaaatctcaataatctaactacaatcatgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGG
  || |  ||   ||  || || ||  |  || ||||| || ||  | | |  || | |    ||||||| |  || || |   |    || || || | |||||||||||||||||||||||   |||||| ||||||| |  | | ||| ||||||| | | ||||||| ||||||||||| ||| | || ||||| || ||
taattagttaatactgcttcacctttcgcatgcacatcccttaggtt-tcacgagtagtgt--aattttgcagcct-aacatgattctcaccattatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATGCGCTGATATGCATCACTAAGCTGGATCGGAAGAAACTATGCTTAGTCGG
















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|88332716|gb|CI660234.1|CI660234
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88689372|gb|CI732948.1|CI732948
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88330039|gb|CI652429.1|CI652429
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88570006|gb|CI661181.1|CI661181
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88691366|gb|CI733949.1|CI733949
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|33807142|gb|CF329453.1|CF329453
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88393631|gb|CI619923.1|CI619923
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88288671|gb|CI663460.1|CI663460
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88717775|gb|CI741285.1|CI741285
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88693267|gb|CI736842.1|CI736842
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88316614|gb|CI622860.1|CI622860
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88691736|gb|CI733814.1|CI733814
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
EST: gi|88689634|gb|CI733210.1|CI733210
EST:     GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAG                         GTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG
genomic: GTCGTACAAGTGGCGTATGGTGATCGCCTACGACGGGACCAAGTTCAAAGgttcttggtc ... catgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcagaacttcagaattttgaaatctcaataatctaactacaatcatgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGG
                                atctaac  putative branch site (score: 2)
              aattttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaactaccttgttgacattatgtgtgaacatcactgagactgtgatcagaacttcagaattttgaaatctcaataatctaactacaatcatgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT