RetrogeneDB ID: retro_cjac_800

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:79984155..79985081(-)
• Located in intron of: ENSCJAG00000021876

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010101
• Aliases: None
• Description: None

Sequence

>retro_cjac_800
ATGAGGGAGATTGTGCTCATGCAAACTGGACAGTGCGGGAACCAGATTGGTGCTAAGTTCTGAGAGGTGATCTCTGATGA
ACATGGCATCAACTCCGCTGGCACCTACCATGGGGACAGTGACCTGTAGCTGGTGTGCATCAATGTGTACTACAACAAGG
TCAGCAGTGGCAGGTACATGGCCTGCACTGTGCTCATGGATCTGGAGCCGGGCACCATGGACTCTGTGTGCTTGGGGCCT
TTTGGGCAGATCTTCAGGCCAGACAACTTCATCTTTGGTCATCGTGGGGCCAAAAACAACTGGGCCTAGGGGTACTACAC
TGAAGGTGGGGAGCTGATGGAGTTTGGTGATGGATGTTGTGAGAAGAGAGGCTGAGAGCTGTGATTGCCTGCAGGGTTTC
CAGCTGACCCACTCCCTGGGTGGGAGGACTGGGTCTGGGATGGGTACCCTTCTCATGGGCAAAATTTGGGAGGAGTACCC
AGACAAGATCATAAACACATTCAGCATTCTGCCCTCATTCAAGGTGTCAAACACCGTGGTGTAGCCCTACAATGCCACCC
TCTCCATCCACAAGCTCATAGGAAATGTGGACAAGATGTTCTGCATCGATAATGAAAAGCTCTGTAACATCTGTTCCAGG
ACCTTAAAACTAACCACACCCACATACGGTGACCTGAATCACCTGGTGTCTGCTACCATGAGTGGGGTCACCACGTGCCC
GCGCTTCCCCGGGCCAGCTGAATGCTGACCTGCCAAAGCTGTCTGTGAACATGGTTCCATTTCCCTGGCTGCAGTTCTTC
ATGCCTGGCTTTGCCTTGCTGACCAGCTGGGGCAGCCAGCAATACCCGGCCCTGATCGTGGCTGAACTCACCCAGCAGCT
GTCTGATGTTAAGAATATGATGGCCGCCTGTGACTGCCCCCGCCAC

Alignment

ORF - retro_cjac_800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.55 %
• Parental protein coverage: 70.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVLTQTGQCGNQIGAKFWEVISDEHGIDPVGTYHGDSDLQLERINVYYNEASGGRYVARAVLVDLEP
          MREIVL.QTGQCGNQIGAKF.EVISDEHGI...GTYHGDSDL.L..INVYYN..S.GRY.A..VL.DLEP
Retrocopy MREIVLMQTGQCGNQIGAKF*EVISDEHGINSAGTYHGDSDL*LVCINVYYNKVSSGRYMACTVLMDLEP

Parental  GTMDSVRSGPFGQIFRPDNFIFGQCGAGNNWAKGYYTEGAELMES-VMDVVRKEAESCDCLQGFQLTHSL
          GTMDSV..GPFGQIFRPDNFIFG..GA.NNWA.GYYTEG.ELME..VMDVVR.EAESCDCLQGFQLTHSL
Retrocopy GTMDSVCLGPFGQIFRPDNFIFGHRGAKNNWA*GYYTEGGELMEF>VMDVVRREAESCDCLQGFQLTHSL

Parental  GGGTGSGMGTLLMGKIREEYPDRIINTFSILPSPKVSDTVVEPYNATLSIHQLIENADETFCIDNEALYN
          GG.TGSGMGTLLMGKI.EEYPD.IINTFSILPS.KVS.TVV.PYNATLSIH.LI.N.D..FCIDNE.L.N
Retrocopy GGRTGSGMGTLLMGKIWEEYPDKIINTFSILPSFKVSNTVV*PYNATLSIHKLIGNVDKMFCIDNEKLCN

Parental  ICSRTLKLTTPTYGDLNHLVSATMSGVTTCLRF-PGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGS
          ICSRTLKLTTPTYGDLNHLVSATMSGVTTC.RF.PGQLNADL.KL.VNMVPFP.L.FFMPGFA.LTS.GS
Retrocopy ICSRTLKLTTPTYGDLNHLVSATMSGVTTCPRF>PGQLNADLPKLSVNMVPFPWLQFFMPGFALLTSWGS

Parental  QQYRALTVAELTQQLFDAKNMMAACD-PRH
          QQY.AL.VAELTQQL.D.KNMMAACD.PRH
Retrocopy QQYPALIVAELTQQLSDVKNMMAACDCPRH

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	1.40 RPM	0.00 RPM
SRP051959_heart	0.53 RPM	0.00 RPM
SRP051959_kidney	0.58 RPM	0.02 RPM
SRP051959_liver	0.50 RPM	0.00 RPM
SRP051959_lung	0.78 RPM	0.00 RPM
SRP051959_lymph_node	0.80 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.52 RPM	0.00 RPM
SRP051959_spleen	0.78 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_800 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_800 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004826	2 retrocopies	retro_cjac_1632, retro_cjac_2667,
Callithrix jacchus	ENSCJAG00000010101	1 retrocopy	retro_cjac_800 ,
Callithrix jacchus	ENSCJAG00000010530	1 retrocopy	retro_cjac_1144,
Callithrix jacchus	ENSCJAG00000011697	1 retrocopy	retro_cjac_3284,
Callithrix jacchus	ENSCJAG00000017637	1 retrocopy	retro_cjac_1649,
Dipodomys ordii	ENSDORG00000015889	1 retrocopy	retro_dord_254,
Homo sapiens	ENSG00000173213	1 retrocopy	retro_hsap_3733,
Homo sapiens	ENSG00000173876	1 retrocopy	retro_hsap_3944,
Mus musculus	ENSMUSG00000016255	1 retrocopy	retro_mmus_1109,
Pongo abelii	ENSPPYG00000011180	1 retrocopy	retro_pabe_3250,