RetrogeneDB ID: retro_ogar_3452

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873850.1:362993..364112(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: THUMPD3
• Ensembl ID: ENSOGAG00000017111
• Aliases: None
• Description: THUMP domain containing 3 [Source:HGNC Symbol;Acc:24493]

Sequence

>retro_ogar_3452
GAAGAAGTTCTAAAGGATTTTGAAGACTTGGCTAGAAAACTCCCATGGTCAGAGCCTTTGAAAGTATGGAAAATTAACAC
CACTTTTAAGAAAAAAAAAACAAAGCACAAAAAGATAAATCAAAATTCAAGTAAAGGGAAGATTGATAATGGAAAAGAAG
ACAAAACAGATGAGGCCGATGTTAAAAAAGAGTTGCCTGGCAATGCTTTAGATTCACATATCTTAGATTATTATGAAAAT
CCAGCCATCAAAGAGGAGATATCTACATTGGTAGGTGATGATTTGGCATCTTGCAAAGATGAGACTGATGAGAGTGCAAA
ACAAGAAACTGAGCCTCAAGTGCTAAAATTTAGAGTCACATGCAACAGGGCAGGAGAGAAACATTGCTTTACCTCCAATG
AGGCTGCAAGAGATTTTGGAGGTGCTATTCAAGATTATTTTCAGTGGAAGGCTGACATGACCAACTTTGATGTGGAGGTT
CTTTTGAATATCCATGGTAATGAAATCATTGTGGGCATTGCTTTGACTGAAGAGAGTCTCCACCGAAGAAATATCACACA
TTTTGGACCTACAACTCTTAGATCAACTCTTGCCTATGGGATGCTCAGGCTCTGTGATCCTCTGCCTTATGATATAATAG
TCGATCCAATGTGTGGAACAGGGGCAATACCAATAGAGGGAGCGACTGAATGGTCTGACTGTTACCATATTGCTGGCGAT
AATAATCCACTGGCTGTAAATAGAGCAGCAAATAACATCTCATCTTTATTGACCAAGAGCCAAAATAAAGAAGGGAAACC
ATCGTGGGGTTTGCCCATAGATGCTGTTCAATGGGATATCTGCAATCTGCCCTTAAGAACAGGCTCAGTGGATATTATTG
TAACAGATTTGCCGTTTGGAAAAAGGATGGGCTCCAAGAAGAGAAACTGGAACCTTTATCCAGCTTGCCTACGGGAGATG
AGCCGTGTCTGCACACCTGCAACAGGCAGAGCTGTACTTCTTACTCAGGACACGAAGTGCTTTACCAAGGCATTATCTGG
AATGCGACATGTATGGCGAAAGGTGGATACAGTCTGGGTGAACATTGGGGGCCTTCGTGCTGCAGTTTATGTTCTGGGA

Alignment

ORF - retro_ogar_3452 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.71 %
• Parental protein coverage: 90.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEVLKDFEDLARKLPWSEPLKVWKINTTFKKKKTKRKKINQNSSKGKIDNGKEDKTDEADVKKELPGNAL
          EEVLKDFEDLARKLPWSEPLKVWKINTTFK............SSKGKIDNGKEDKTDEADVKKELPGNAL
Retrocopy EEVLKDFEDLARKLPWSEPLKVWKINTTFKXXXXXXXXXXXXSSKGKIDNGKEDKTDEADVKKELPGNAL

Parental  DSHILDYYENPAIKEEISTLVGDDLASCKDETDESAKQETEPQVLKFRVTCNRAGEKHCFTSNEAARDFG
          DSHILDYYENPAIKEEISTLVGDDLASCKDETDESAKQETEPQVLKFRVTCNRAGEKHCFTSNEAARDFG
Retrocopy DSHILDYYENPAIKEEISTLVGDDLASCKDETDESAKQETEPQVLKFRVTCNRAGEKHCFTSNEAARDFG

Parental  GAIQDYFQWKADMTNFDVEVLLNIHGNEIIVGIALTEESLHRRNITHFGPTTLRSTLAYGMLRLCDPLPY
          GAIQDYFQWKADMTNFDVEVLLNIHGNEIIVGIALTEESLHRRNITHFGPTTLRSTLAYGMLRLCDPLPY
Retrocopy GAIQDYFQWKADMTNFDVEVLLNIHGNEIIVGIALTEESLHRRNITHFGPTTLRSTLAYGMLRLCDPLPY

Parental  DIIVDPMCGTGAIPIEGATEWSDCYHIAGDNNPLAVNRAANNISSLLTKSQNKEGKPSWGLPIDAVQWDI
          DIIVDPMCGTGAIPIEGATEWSDCYHIAGDNNPLAVNRAANNISSLLTKSQNKEGKPSWGLPIDAVQWDI
Retrocopy DIIVDPMCGTGAIPIEGATEWSDCYHIAGDNNPLAVNRAANNISSLLTKSQNKEGKPSWGLPIDAVQWDI

Parental  CNLPLRTGSVDIIVTDXTFFYRMGSKKRNWNLYPACLREMSRVCTPATGRAVLLTQDTKCFTKALSGMRH
          CNLPLRTGSVDIIVTD..F..RMGSKKRNWNLYPACLREMSRVCTPATGRAVLLTQDTKCFTKALSGMRH
Retrocopy CNLPLRTGSVDIIVTDLPFGKRMGSKKRNWNLYPACLREMSRVCTPATGRAVLLTQDTKCFTKALSGMRH

Parental  VWRKVDTVWVNIGGLRAAVYVLG
          VWRKVDTVWVNIGGLRAAVYVLG
Retrocopy VWRKVDTVWVNIGGLRAAVYVLG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3452 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008538	1 retrocopy	retro_mluc_1991,
Macaca mulatta	ENSMMUG00000017307	1 retrocopy	retro_mmul_1600,
Otolemur garnettii	ENSOGAG00000017111	1 retrocopy	retro_ogar_3452 ,
Sus scrofa	ENSSSCG00000030273	1 retrocopy	retro_sscr_873,
Tupaia belangeri	ENSTBEG00000003450	7 retrocopies	retro_tbel_2328, retro_tbel_2589, retro_tbel_3717, retro_tbel_4362, retro_tbel_4489, retro_tbel_4567, retro_tbel_969,