RetrogeneDB ID: retro_cjac_877

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:111791837..111792773(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000009209
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OR4A5
• Ensembl ID: ENSCJAG00000009212
• Aliases: None
• Description: olfactory receptor, family 4, subfamily A, member 5 [Source:HGNC Symbol;Acc:15162]

Sequence

>retro_cjac_877
ATGAGACAGAGTAACAATGTTACAGAATTTGTCCTCCTGGGGCTCACTCAGGATCCTGATGTGCAAAAAGCATTATTTGC
CATGCTTTTACTCATATACATTGTGACAATGGTGGGAAATCTCCTCATTGTGGTGACTACTCTAGGCAGCCCCTCCTTGG
GCTCCCCAATGTACTTCTTCCTTGCCTACTTGTCACTTCTGGATGCCATATATTCCACTGCCATGTCACCCAAATTGATG
ATGGACTTACTCTGTGATAAAAACAGCATTTCCTTCTCAGCTTGCATGGGTCAGCTCTTCATAGAACACTTACTTGGTGG
TGCAGAGGTCTTCCTTCTGGTACTGATGGCCTTTGATCGCTATGTGGCCATCACTAAGCCACTGCAGTATTTGAATATCA
TGAATCGACAGGTTTGCATCTTTCTCTTGGTGGTGGCCGTGGTTGGAGGTTTTGTGCACTCTGTGGTTCAAATTGTTATT
GTGTACAGTCTACCATTCTGTGGCCCCAATGTCATTGACCATTTCATCTGTGACATGTACCCATTATTGGAACTGGCGTG
CACTGACACCTACTTTATAGGCCTCACTGTGGTTGCCAATGGTGGAACAATCTGTATGGTTGTCTTTACCTTTCTGCTAA
TCTCCTACGGAGTCATCCTAAACTCCCTTAAAACTTACAGTCAGGAAGGGAGGCGTAAAGCCCTGTCTACCTGCAGCTCC
CACATCACCGTGGTGGTCTTGTTTTTTGTTCCCTGTATTTTCATGTACGTTAGACCAGTTTCCAACTTTCCCTTTGATAA
ATTCGTGACTGTGTTTTATACAATTATCACACCCATGTTGAATCCTTTAATGTACACATTGAGAAATTCAGAGATGAAAA
ATGCTATGAAAAAACTCTTGTGTAAAAAGTTAAATATAGTTAGAATGAGTTTCTCC

Alignment

ORF - retro_cjac_877 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.17 %
• Parental protein coverage: 99.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRQKNNITEFVLLGFSQDPDVQKALFVMFLLTYFMTMVGNLLIVVTITASPSLGSPMYFFLACLSFIDAA
          MRQ.NN.TEFVLLG..QDPDVQKALF.M.LL.Y..TMVGNLLIVVT...SPSLGSPMYFFLA.LS..DA.
Retrocopy MRQSNNVTEFVLLGLTQDPDVQKALFAMLLLIYIVTMVGNLLIVVTTLGSPSLGSPMYFFLAYLSLLDAI

Parental  YSTIISPKLTVDLLCDKKTISLPACMGQLFIDHLFGGAEIFLLVVMACDRYMAICKPLHYLTIMNRQVCI
          YST..SPKL..DLLCDK..IS..ACMGQLFI.HL.GGAE.FLLV.MA.DRY.AI.KPL.YL.IMNRQVCI
Retrocopy YSTAMSPKLMMDLLCDKNSISFSACMGQLFIEHLLGGAEVFLLVLMAFDRYVAITKPLQYLNIMNRQVCI

Parental  LMLVLAMIGGLVHSVFQIVVVYSLPFCGPNVIDHFYCDMYPLLELTCTDTYFIGLTVVFNGGAICMIIFT
          ..LV.A..GG.VHSV.QIV.VYSLPFCGPNVIDHF.CDMYPLLEL.CTDTYFIGLTVV.NGG.ICM..FT
Retrocopy FLLVVAVVGGFVHSVVQIVIVYSLPFCGPNVIDHFICDMYPLLELACTDTYFIGLTVVANGGTICMVVFT

Parental  LLLISYGVILNSLKTYSHEGRRKALSTCSSHIAVVVLFFVPCIFIYVRPVSNFPVDKFITVFYTVISPMM
          .LLISYGVILNSLKTYS.EGRRKALSTCSSHI.VVVLFFVPCIF.YVRPVSNFP.DKF.TVFYT.I.PM.
Retrocopy FLLISYGVILNSLKTYSQEGRRKALSTCSSHITVVVLFFVPCIFMYVRPVSNFPFDKFVTVFYTIITPML

Parental  NPFIYTLRNSEMRNAIEKLLCKKLTIVRIRVS
          NP..YTLRNSEM.NA..KLLCKKL.IVR...S
Retrocopy NPLMYTLRNSEMKNAMKKLLCKKLNIVRMSFS

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_877 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_877 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009212	1 retrocopy	retro_cjac_877 ,
Rattus norvegicus	ENSRNOG00000046433	1 retrocopy	retro_rnor_1896,