RetrogeneDB ID: retro_ogar_2091

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873590.1:3287381..3287895(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED8
• Ensembl ID: ENSOGAG00000001865
• Aliases: None
• Description: mediator complex subunit 8 [Source:HGNC Symbol;Acc:19971]

Sequence

>retro_ogar_2091
GGACAGACTCCCATTTTTAGCCTTGGGGTGATCCCTGACCATCTGAGAACCAAGCCTGGCCCTGAGGTTGAAGAGCAGGA
GCAACAGCCAACAACAGACACTGGCCACAGGGGTGCGGCTGCAGCTGAGAGGCAGATCCAGAACTAGAACAAGATGTGTT
CCAGTCTCCCAGAGAAAATCAGCAAAGAGGAGTGAGATCTGAGAGTGGAGGTCTCCGGCCAATACGCAGATCTCTAACCC
TGCCCACACCAATGCCATGGTGGGAGCTGTGGCCTTTGGGAAGGGGCTGTCTAATTGGAGCCCTTCAGGCAGCAGTGGTC
CTGGCCAGCTAGGCCAGCCAGAAACTGGACCAATCCTTGCAGGAGCCTCAGGATTTCAGAGGTGCAGATGGCAGGAGTGC
CATGCCAGCAGCAGCCAGTGCTTGGTGGGGTGCAGATGGCCCGAGCAGGAGAGCAGGGAAAACACCGAATGGGTGAAAAC
CACCACCAAGGCGGCTTCAGGGCATCCCTGCCAG

Alignment

ORF - retro_ogar_2091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.98 %
• Parental protein coverage: 64.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GRVPVFSHEVVPDHLRTKPDPEVEEQEKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERE-SES
          G..P.FS..V.PDHLRTKP.PEVEEQE.Q.TTD....GA.AA..QIQ..NKMCS.L.EKISKEE...SES
Retrocopy GQTPIFSLGVIPDHLRTKPGPEVEEQEQQPTTDTGHRGAAAAERQIQN*NKMCSSLPEKISKEE*D<SES

Parental  GGLRP-NKQTFNPADTNALVAAVAFGKGLSNWRPSGSSGPGQ---PGAGTILAGASGLQ-QVQMAGAPSQ
          GGLRP.N.Q..NPA.TNA.V.AVAFGKGLSNW.PSGSSGPGQ...P..G.ILAGASG.Q..VQMAG.P.Q
Retrocopy GGLRP<NTQISNPAHTNAMVGAVAFGKGLSNWSPSGSSGPGQLGQPETGPILAGASGFQ<EVQMAGVPCQ

Parental  QQPMLSGVQMAQAGQ-PGKMPSG-IKTNIKSASMHPYQ
          QQP.L.GVQMA.AG...GK.P.G..KT..K.AS.HP.Q
Retrocopy QQPVLGGVQMARAGE<AGKTPNG<VKTTTKAASGHPCQ

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_2091 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005237	1 retrocopy	retro_cfam_458,
Macropus eugenii	ENSMEUG00000013567	1 retrocopy	retro_meug_1813,
Myotis lucifugus	ENSMLUG00000012621	1 retrocopy	retro_mluc_1618,
Monodelphis domestica	ENSMODG00000011310	1 retrocopy	retro_mdom_1131,
Oryctolagus cuniculus	ENSOCUG00000027895	2 retrocopies	retro_ocun_1088, retro_ocun_67,
Otolemur garnettii	ENSOGAG00000001865	1 retrocopy	retro_ogar_2091 ,
Ictidomys tridecemlineatus	ENSSTOG00000009737	1 retrocopy	retro_itri_818,