RetrogeneDB ID: retro_ogar_3092

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873713.1:149977..150876(+)
• Located in intron of: ENSOGAG00000014311

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC47
• Ensembl ID: ENSOGAG00000006869
• Aliases: None
• Description: coiled-coil domain containing 47 [Source:HGNC Symbol;Acc:24856]

Sequence

>retro_ogar_3092
GATGATGGAACTAACAAAGAAGCCACAAGCACAGGAAAGTTGAACCAGAAGAATGAGCACATCTATAACCTATGGTGTTC
TGGTCAAGTGTGCTGTGAGGGCATGCTTATCTAGCTGAGATTCCTCAAGAGACAAGACTTACTGAATGTCCTGGCCCGGA
TGATGAGGCCAGTGAGTGATCAAATGCAAATAAAAGTAACCATGAATGATGAAGACATGGATACCTATGTGTTTGCTGTT
GGCACATGGAAGGCCTTGGTGCAACTGCAAAAGAAATGCAGGACCTGAGTGTGTTTTGTAGTGATAAACCTAAATCTGAA
GCAAAGTATGGATTGCCAGACTCCTTGGCCATCCTGTCAGAGATAGGAGAAGTCACAGAGGGAATGATGGATACAAAGAT
GGTTCACTTTCTTACACACTATGCTGACAAGATTGAATCCATCCACTTTTCAGACCAGTTCTCTGGTCCAAAAATTATGC
AAGAGGAAGGTCAGTCTTTGAAGCTACCTGACACTAAGAGGACACTATTGTTTACATTTAATGTGCCTGGATCAGATAAC
ACTTACCCAAAGGATATGGAGGCTTTGCTATCCCTGATGAACATGATGATTTACTCTATTGATAAAGCCAAAAAGTTCCG
ACTCAACAGAGAAGGCAAACAAAAAGCAGATAAGAACCATACTCGTGTAGAAGAGAACTTCTTGAAGCTGACACATGTGC
AAAGACAGGAAGCTGCACAGTCTCGGCTGGAGAAAAAGAAAAGGGCAGAGAAGGAGTGAATCATGAATAAGGAAGTTAAT
GAGGAACAGCGCAGGCTGGAAGAAGCTCCTTTGAGGCGTGAGCAAAAGAAGTCAGAGAAGCAGCAAATGAAAATGAAACA
AATCAAAGTAAAAGCCATG

Alignment

ORF - retro_ogar_3092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.43 %
• Parental protein coverage: 62.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DDGTNKEATSTGKLNQENEHIYNLWCSGRVCCEGMLIQLRFLKRQDLLNVLARMMRPVSDQVQIKVTMND
          DDGTNKEATSTGKLNQ.NEHIYNLWCSG.VCCEGMLI.LRFLKRQDLLNVLARMMRPVSDQ.QIKVTMND
Retrocopy DDGTNKEATSTGKLNQKNEHIYNLWCSGQVCCEGMLI*LRFLKRQDLLNVLARMMRPVSDQMQIKVTMND

Parental  EDMDTYVFAVGTRKALVRLQK-EMQDLSEFCSDKPKSGAKYGLPDSLAILSEMGEVTEGMMDTKMVHFLT
          EDMDTYVFAVGT.KALV.LQK.EMQDLS.FCSDKPKS.AKYGLPDSLAILSE.GEVTEGMMDTKMVHFLT
Retrocopy EDMDTYVFAVGTWKALVQLQK<EMQDLSVFCSDKPKSEAKYGLPDSLAILSEIGEVTEGMMDTKMVHFLT

Parental  HYADKIESVHFSDQFSGPKIMQEEGQPLKLPDTKRTLLFTFNVPGSGNTYPKDMEALLPLMNMVIYSIDK
          HYADKIES.HFSDQFSGPKIMQEEGQ.LKLPDTKRTLLFTFNVPGS.NTYPKDMEALL.LMNM.IYSIDK
Retrocopy HYADKIESIHFSDQFSGPKIMQEEGQSLKLPDTKRTLLFTFNVPGSDNTYPKDMEALLSLMNMMIYSIDK

Parental  AKKFRLNREEKGKQKADKNRARVEENFLKLTHVQRQEAAQSRREEKKRAEKERIMNEEDPEKQRRLEEAA
          AKKFRLNRE..GKQKADKN..RVEENFLKLTHVQRQEAAQSR.E.KKRAEKE.IMN.E..E.QRRLEEA.
Retrocopy AKKFRLNRE--GKQKADKNHTRVEENFLKLTHVQRQEAAQSRLEKKKRAEKE*IMNKEVNEEQRRLEEAP

Parental  LRREQKKLEKKQMKMKQIKVKAM
          LRREQKK.EK.QMKMKQIKVKAM
Retrocopy LRREQKKSEKQQMKMKQIKVKAM

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_3092 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000006869	1 retrocopy	retro_ogar_3092 ,
Rattus norvegicus	ENSRNOG00000009006	1 retrocopy	retro_rnor_2236,
Tupaia belangeri	ENSTBEG00000009955	1 retrocopy	retro_tbel_159,