RetrogeneDB ID: retro_cjac_1898

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:32317457..32318669(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPTOR
• Ensembl ID: ENSCJAG00000005497
• Aliases: DEPTOR, DEPDC6
• Description: None

Sequence

>retro_cjac_1898
ATGGAAGAGGGTGGCAGCGCTGGCAGTGACAGCAGCACCAGCGGAAGTGGTGGGGCGCAGCAAAGGGAGCTGGAGCACAT
GGCTGAGGTCTTGGTCACCGGGGAGCAGCTACGGCTCAGGCTGCATGAAGAAAAGGTTATTAAAGATAGACGTCATCATC
TCAAGACCTACCCAAACTGTTTTGTCACAAAAGAACTGATTGGCTGATTGGACACAAAGAGGCTTCCGACAGAGAGATGG
CAATTACACTCATGCAGAAATTAGCAGACCAATGCATTATTCACCATGTGTGTGATGAGCATAAGGAATTCAAGGATGTC
AAACTCTTCTACCGCTTTAGAAAGGATGACGGCACCTTCCCATTGGATAACGAAGTGAAGGCCTTTATGAGAGGACAGAG
GCTGTATGAAAAGCGGATGAGCCCTGAAAACACCCTTCTGCAGCCCAGGGAGAAGGAAGGGGTCAAGTATGAGTGCACCC
TCATGCAATCTGAATTCCTGGACTGGCTGGTTCAGGAAGGTGAGGCCACCACCAGGAAAGAGGCAGAGCCCCTCTGCCAC
CAGCTTATGGAGCATGGCATCATCCAGCGTGTGTCCAACAAGCACCCATTTGTGGACAGCAATCTTCTCTACCAGTTCAG
AATGAACTTCCGGTGGAGGCAAAGACTGATAGAGCTGATCAATGAAAAGTCTTCCTCCTCCTAGGAAACTCATGAGAGCC
CCTTCTGCCTGAGGAAGCAGAGCCATGACAATCGGAAATCTACCAGCTTTATGTCAGTGAGCCCCAGCAAGGAGATCAAG
ATTGTGTCTGCAGTGAGGAGGAGCAGCACGAGCACCTGCGGCAGCAGCGAGTACTTCCGCAGCAGCCCCACCCTCAGCAG
CAGCCCCCCGGTGCCCTGCAACCCCAAGTCTGTGCTGTAGAGACCTGTCACGTCTGAGGAACTCCTCACTCCCGGGGCTC
CGTATGCAAGGAAGACATTCATGATTGTTGGTGACTCGGTTGGCTGCGGTTTTGTGGTGTGAGGAAGTTAAGCCCTGCCA
CATCCAGGATGTCGACCCCAGTGGCCCTGCAGCCACTGCAGCAGGAATGAAGGTCTGTCAGTTTGTCGTATCTGTCAATG
GGCTCAATGTCCTGCATGTAGACTACCGGACCATGAGCAATCTGATCCTAATGGGCCCACGGACAATTGTCATGGAAGTC
ATGGAGGAGTTA

Alignment

ORF - retro_cjac_1898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.29 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEEGSSAGSAGSDSRTSGSGGAQQRELERMAEVLVTGEQLRLRLHEEKVIKDRRHHLKTY-PNCFVAKEL
          MEEG...GSAGSDS.TSGSGGAQQRELE.MAEVLVTGEQLRLRLHEEKVIKDRRHHLKTY.P..F..K..
Retrocopy MEEG---GSAGSDSSTSGSGGAQQRELEHMAEVLVTGEQLRLRLHEEKVIKDRRHHLKTY<PKLFCHKRT

Parental  IDWLIEHKEASDRETAIKLMQKLADRGIIHHVCDEHKEFKDVKLFYRFRKDDGTFPLDNEVKAFMRGQRL
          .DWLI.HKEASDRE.AI.LMQKLAD..IIHHVCDEHKEFKDVKLFYRFRKDDGTFPLDNEVKAFMRGQRL
Retrocopy -DWLIGHKEASDREMAITLMQKLADQCIIHHVCDEHKEFKDVKLFYRFRKDDGTFPLDNEVKAFMRGQRL

Parental  YEKLMSPENTLLQPREEEGVKYERTFMASEFLDWLVQEGEATTRKEAEQLCHRLMEHGIIQHVSNKHPFV
          YEK.MSPENTLLQPRE.EGVKYE.T.M.SEFLDWLVQEGEATTRKEAE.LCH.LMEHGIIQ.VSNKHPFV
Retrocopy YEKRMSPENTLLQPREKEGVKYECTLMQSEFLDWLVQEGEATTRKEAEPLCHQLMEHGIIQRVSNKHPFV

Parental  DSNLLYQFRMNFRRRRRLMELLNEKSPSSQETHDSPFCLRKQSHDNRKSTSFMSVSPSKEIKIVSAVRRS
          DSNLLYQFRMNFR.R.RL.EL.NEKS.SS.ETH.SPFCLRKQSHDNRKSTSFMSVSPSKEIKIVSAVRRS
Retrocopy DSNLLYQFRMNFRWRQRLIELINEKSSSS*ETHESPFCLRKQSHDNRKSTSFMSVSPSKEIKIVSAVRRS

Parental  SMSSCGSSGYFSSSPTLSSSPPVLCNPKSVLKRPVTSEELLTPGAPYARKTFTIVGDAVGWGFVVRGS-K
          S.S.CGSS.YF.SSPTLSSSPPV.CNPKSVL.RPVTSEELLTPGAPYARKTF.IVGD.VG.GFVV.GS.K
Retrocopy STSTCGSSEYFRSSPTLSSSPPVPCNPKSVL*RPVTSEELLTPGAPYARKTFMIVGDSVGCGFVV*GS>K

Parental  PCHIQAVDPSGPAA-AAGMKVCQFVVSVNGLNVLHVDYRTVSNLILTGPRTIVMEVMEEL
          PCHIQ.VDPSGPAA.AAGMKVCQFVVSVNGLNVLHVDYRT.SNLIL.GPRTIVMEVMEEL
Retrocopy PCHIQDVDPSGPAATAAGMKVCQFVVSVNGLNVLHVDYRTMSNLILMGPRTIVMEVMEEL

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	0.02 RPM	10.14 RPM
SRP051959_heart	0.00 RPM	2.19 RPM
SRP051959_kidney	0.00 RPM	31.11 RPM
SRP051959_liver	0.00 RPM	13.82 RPM
SRP051959_lung	0.02 RPM	17.32 RPM
SRP051959_lymph_node	0.00 RPM	3.26 RPM
SRP051959_skeletal_muscle	0.00 RPM	63.37 RPM
SRP051959_spleen	0.00 RPM	6.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1898 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1898 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005497	1 retrocopy	retro_cjac_1898 ,
Dasypus novemcinctus	ENSDNOG00000015660	1 retrocopy	retro_dnov_747,
Ictidomys tridecemlineatus	ENSSTOG00000013845	1 retrocopy	retro_itri_669,