RetrogeneDB ID: retro_ogar_403

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873521.1:1382314..1383101(+)
• Located in intron of: ENSOGAG00000011034

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1C2
• Ensembl ID: ENSOGAG00000009748
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2 [Source:HGNC Symbol;Acc:18264]

Sequence

>retro_ogar_403
ATGTCAGAGTTTTGGTTAATTTCTGCCCCTGTCAATAAGGAAAATTTACAAGCTCTGGAGAAGATAAATCCTGTAACCTC
CAAGTCCAACCTGTCTTACAATACCAAATTCACTATTCCTGATTTCAAGATGGAGACCTTGGAACTCCTAGTAGGCCTCT
TAGATGAGTTGGGGAGACTTGATACCTTTGCTAAAAGCCTCATAAAGAGGATGGCCCAGAGCATGGCAGAAGAGATGAAG
GACTCAAAGGGGAAGGTCCAGGAGAACCTTCTGGCCAATGGAGTCAATCTGATGTCCTTCGTGACTTACTCTGAAGGGGA
CATGGGAAAATAATCCCACAAAGCAGCTGTTCATGGTGTGGTAGACACACTAGCGAAGCAACTGGCACAGATTAAGATAG
ATCTGAAGGCCCAGATGGCTGCCTACAATACTCTAAGACAACCTTGGAGAACCTGAGAAGAAATCCATGGAGAACCTCTT
CACTTAGACACTGAGTGAGTTACACTGTGAGCAAAGAAGATTTCATGCTGGATTCTGAATATCTCATCACCCTCCTTGTC
ATTGCCTCCAAACCAAGCTACACACAATGAAAAAAACCTGTGAATCCCCCTTGGACATGGTAGTCCCTTGGTCAACCAAA
CTGATTTCTGAAGACAATGAGGGTGGCCTCTTCAGAATGATTGTGTTTTGAAAAGCAACTAACAATTTTAAAAGCAAAGC
CAAAGAAAACAAGTTCACTGCCCATGAATTTTACTATGATAAAAACAAAATTAAAAAGGAAAGGAAG

Alignment

ORF - retro_ogar_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.94 %
• Parental protein coverage: 61.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEFWLISAPGDKENLQALERMNTVTSKSNLSYNTKFAIPDFKVGTLDSLVGLSDELGKLDTFAESLIKR
          MSEFWLISAP..KENLQALE..N.VTSKSNLSYNTKF.IPDFK..TL..LVGL.DELG.LDTFA.SLIKR
Retrocopy MSEFWLISAPVNKENLQALEKINPVTSKSNLSYNTKFTIPDFKMETLELLVGLLDELGRLDTFAKSLIKR

Parental  MAQSVAEVMEDSKGKVQENLLANGVDLTSFVTHFEWDMAKYPAKQPLVGVVDTLAKQLAQIETDLKTRTA
          MAQS.AE.M.DSKGKVQENLLANGV.L.SFVT..E.DM.K...K....GVVDTLAKQLAQI..DLK...A
Retrocopy MAQSMAEEMKDSKGKVQENLLANGVNLMSFVTYSEGDMGK*SHKAAVHGVVDTLAKQLAQIKIDLKAQMA

Parental  AYNTL-KTTLENLEKKSMGNLFTRT-LSDIVSKEDFVLDSEYLITLLVIVPKPNYTQ-WQKTYESLSDMV
          AYNTL.KTTLENL..........R...S..VSKEDF.LDSEYLITLLVI..KP.YTQ...KT.ES..DMV
Retrocopy AYNTL<KTTLENLRRNPWRTSSLRH*VSYTVSKEDFMLDSEYLITLLVIASKPSYTQ<MKKTCESPLDMV

Parental  VPRSTKLIAEDNEGGLFTVTLFRKVIDDFKSKAKENKFTVREFYYDENEIKRERE
          VP.STKLI.EDNEGGLF....F.K....FKSKAKENKFT..EFYYD.N.IK.ER.
Retrocopy VPWSTKLISEDNEGGLFRMIVF*KATNNFKSKAKENKFTAHEFYYDKNKIKKERK

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_403 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001927	1 retrocopy	retro_btau_1823,
Callithrix jacchus	ENSCJAG00000006660	2 retrocopies	retro_cjac_1089, retro_cjac_3461,
Monodelphis domestica	ENSMODG00000014803	1 retrocopy	retro_mdom_2006,
Otolemur garnettii	ENSOGAG00000009748	1 retrocopy	retro_ogar_403 ,
Sarcophilus harrisii	ENSSHAG00000009886	1 retrocopy	retro_shar_33,