RetrogeneDB ID: retro_ogar_3005

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873695.1:2431297..2431912(+)
• Located in intron of: ENSOGAG00000028605

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC3
• Ensembl ID: ENSOGAG00000003503
• Aliases: None
• Description: THO complex 3 [Source:HGNC Symbol;Acc:19072]

Sequence

>retro_ogar_3005
GGAGAGAGCATTAATAACTCCTGGAGTCCAAATAGGCAGACCATTGCTGTAGGCAACAAGGATGATGTGGTGACCTTTAT
TGATGCCAAGACACAACATTCCAAAGCTAAAGAGCAGTTCCAAGTTTGAGGTGAATGAAATCTGTTGGAACAATGACTAT
AATGTGTTCTTCCTGACAAATGGCAACAGTTATATCAACATCCTCAGCTACCCAGAACTGAAGCCTGTGCAGTCCATCAA
GGCCCATCCTTCTAACTGCATCTGTGTGAAGTTTAACCTCATGGGGAAATACTTTGCTACAGGAAGTGCAGATGCTTTGG
TCAGCCTTTGGGATGTGGTAGTATGTGTTCGGTGCTTTTCTAGGCTGGATTGGCCTGTGAGGACACCCAGTTTTAGCCAT
GATGCCGAAGATGCCGGCATCAGCATCAGAAGATCATTTTATTGACATTGCTGAAGTAGACATAGGAGACAAGCTGTGGG
AGGTGCAGTGTGAGTCTCCAACCTTCACTGTGGCACCCCAAAAGGCCTCTGCCAGCATTTGCCTGTGATGATAAAGATGG
TAAATATGATAGCAGTCGGGAAGCTGAAACTGTGAAGCTGTTTCGACTCCCTGAT

Alignment

ORF - retro_ogar_3005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.94 %
• Parental protein coverage: 59.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GENINICWSPDGQTIAVGNKDDVVTFIDAKTHRSKAEEQF-KFEVNEISWNNDNNMFFLTNGNGCINILS
          GE.IN..WSP..QTIAVGNKDDVVTFIDAKT..SKA.EQF.KFEVNEI.WNND.N.FFLTNGN..INILS
Retrocopy GESINNSWSPNRQTIAVGNKDDVVTFIDAKTQHSKAKEQF>KFEVNEICWNNDYNVFFLTNGNSYINILS

Parental  YPELKPVQSINAHPSNCICIKFDPMGKYFATGSADALVSLWDVDELVCVRCFSRLDWPVRTLSFSHDG-K
          YPELKPVQSI.AHPSNCIC.KF..MGKYFATGSADALVSLWDV...VCVRCFSRLDWPVRT.SFSHD..K
Retrocopy YPELKPVQSIKAHPSNCICVKFNLMGKYFATGSADALVSLWDV--VVCVRCFSRLDWPVRTPSFSHDA>K

Parental  MLASASEDHFIDIAEVETGDKLWEVQCESPTFTVAWHPKR-PLLAFACDDKDGKYDSSREAGTVKLFGLP
          M.ASASEDHFIDIAEV..GDKLWEVQCESPTFTVA..P...PL.AFACDDKDGKYDSSREA.TVKLF.LP
Retrocopy MPASASEDHFIDIAEVDIGDKLWEVQCESPTFTVA--PQK>PLPAFACDDKDGKYDSSREAETVKLFRLP

Parental  N
          .
Retrocopy D

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_3005 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006495	2 retrocopies	retro_cjac_1571, retro_cjac_3072,
Macropus eugenii	ENSMEUG00000001068	2 retrocopies	retro_meug_1061, retro_meug_19,
Monodelphis domestica	ENSMODG00000005339	1 retrocopy	retro_mdom_164,
Mus musculus	ENSMUSG00000025872	2 retrocopies	retro_mmus_1821, retro_mmus_441,
Otolemur garnettii	ENSOGAG00000003503	1 retrocopy	retro_ogar_3005 ,
Sarcophilus harrisii	ENSSHAG00000010757	1 retrocopy	retro_shar_4,