RetrogeneDB ID: retro_cjac_1089

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38775387..38776210(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1C2
• Ensembl ID: ENSCJAG00000006660
• Aliases: None
• Description: None

Sequence

>retro_cjac_1089
ATGTCGAAGTTTTGGTTAATTTTTGCCCCTGGCGATAGGGAAAATTTGCAAGCTCTGGAGAGGATGAATACTGTAACCTC
CAAATCCAACCTGTCTTATAATACCAAATTCACTATTCCTGACTTCAAGGAGGGGACCTTGGATTCCCTGGTTGGCCTCT
CTGATGAGTTGGGGAAACTCGACACCTTTGCTGAAAGCCTCATGAGAATGGCTCAGAGCGTGGTGGAAGTCATGGAGGAC
TCGAAGGGGAAGGCACGGGAACACCTCCTGGCAAACGGAGTTGACTTAACCTCCTTTGTGACCCACTTTGAATGGGACAG
GCCAAATATCCTGCCAAGCAGCCGCTCGTGAGCGTGGTGGACACAATAGCCAAGCAACTGGCACAGATCGAGATGGACCT
GAAGTCCTGAAAGGCAGCCTACAACACTCTGAAGACGAACCTGGAGAAGAAATCCATGGGGAACCTCTTCACCCGGACAC
TGAGCGATATTGTGAGCAAAGAGGACTTCGTGCTAGAATCTGAATATCTCGTCACGCTTCTGGTCATTGTCCCCAAACCA
AACTACTCACAATGGCAAAAAACCTATGAATCTCTCTCGGACATGGTGGTCCCTCAATCGACCAAACTCATTACTGAGGA
CAGAAGGGCAGCCTTTTCACTGTGACTCTGTTTCGAAAAGTGATTGAAGATTTCAAAAGCAAAGCCAGAGAAAACAAGTT
CACAGTTCGTGAATTTTACTATGATGAGAAAGAAATTAAAAGGGAAAGGGAGGAGATGGCCCGATCGCTGTGTGATAAGA
AGCAACAGTATGGCCCCCTCCTG

Alignment

ORF - retro_cjac_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 73.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEFWLISAPGDRENLQALERMNTVTSKSHLSYNTKFAIPDFKVGTLDSLVGLSDELGKLDTFAESLIRR
          MS.FWLI.APGDRENLQALERMNTVTSKS.LSYNTKF.IPDFK.GTLDSLVGLSDELGKLDTFAESL.R.
Retrocopy MSKFWLIFAPGDRENLQALERMNTVTSKSNLSYNTKFTIPDFKEGTLDSLVGLSDELGKLDTFAESLMR-

Parental  MAQSVVEVMEDSKGKAQEHLLANGVDLTTFVTHFEWD-MAKYPAKQPLVSVVDTIAKQLAQIETDLKSRT
          MAQSVVEVMEDSKGKA.EHLLANGVDLT.FVTHFEWD..AKYPAKQPLVSVVDTIAKQLAQIE.DLKS..
Retrocopy MAQSVVEVMEDSKGKAREHLLANGVDLTSFVTHFEWD<QAKYPAKQPLVSVVDTIAKQLAQIEMDLKS*K

Parental  AAYNTLKTNLENLEKKSMGNLFTRTLSDIVNKEDFVLDSEYLVTLLVIVPKPNYSQWQKTYESLSDMVVP
          AAYNTLKT...NLEKKSMGNLFTRTLSDIV.KEDFVL.SEYLVTLLVIVPKPNYSQWQKTYESLSDMVVP
Retrocopy AAYNTLKT---NLEKKSMGNLFTRTLSDIVSKEDFVLESEYLVTLLVIVPKPNYSQWQKTYESLSDMVVP

Parental  RSTKLITEDK-EGGLFTVTLFRKVIEDFKSKARENKFTVREFYYDEKEIKREREEMARLLSDKKQQYGPL
          .STKLITED...G.LFTVTLFRKVIEDFKSKARENKFTVREFYYDEKEIKREREEMAR.L.DKKQQYGPL
Retrocopy QSTKLITEDR<KGSLFTVTLFRKVIEDFKSKARENKFTVREFYYDEKEIKREREEMARSLCDKKQQYGPL

Parental  L
          L
Retrocopy L

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	1.82 RPM
SRP051959_heart	0.00 RPM	0.89 RPM
SRP051959_kidney	0.00 RPM	6.17 RPM
SRP051959_liver	0.00 RPM	0.97 RPM
SRP051959_lung	0.05 RPM	9.63 RPM
SRP051959_lymph_node	0.02 RPM	2.19 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.39 RPM
SRP051959_spleen	0.00 RPM	2.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1089 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1089 has 0 orthologous retrocopies within eutheria group .

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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,