RetrogeneDB ID: retro_cjac_3325

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:87788374..87789041(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B2
• Ensembl ID: ENSCJAG00000012698
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa) [Source:HGNC Symbol;Acc:8575]

Sequence

>retro_cjac_3325
CAAGCAGATTCAAATGCAGCAGCTATTCCACACACAGTGGAAGATATTCAAGGAGACAACAGATGGATATCTCAGCACAA
CAGATTTGTCCTGGATGGTAAAGACAAAAAGCCTAATGTTCTGTTTGTGGAAGACCCCATGGTGCAGTTAATGCAGCAAC
ATGAGATATGGCGAGAGCTTTTTTCCCTACTTCACAGAGGAAGTAAGGAAGATACAAGACATGTTTTGTAGAAACTACGG
AATAGAGAACTGGAGAATATTAAACTTAAGGTAATTGCTGTCTAGGTAGGAACAGACAACCATGAAAATGCAGTAAAAGA
GTTAGAAGGTGAGATCAAGGCCATCATTCACTTTATCAGTTTATCAACACAAGACAGCCACAAGTCAAATTCTTCTATTG
GACTTGTTACCTCGAGGTGAGAAGCCCAACCCTTTGAGGCAAAAGGTGAACCAGCTTCTCAAGGTTTCCCCATTAAAGCT
TTCCCATGTATAGGTCTTGCATACAGACAGGGGCTTCATGCACCAGGACAGTGCCATCTCCTGCCACGATATATTTGATT
TTTTGCAGCTTACAGGATAGGGCTATCCAAAGATCTACAAAGCCCTCGGTGAACTGATCATGCAGCTGATGGAGGAAACA
CCCACAGAGAAACAAACCATTATTGCC

Alignment

ORF - retro_cjac_3325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.77 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QGDSNPAAIPHAAEDIQGDDRWMSQHSQQICLDCKDKE-DVLFVGDSMVQLMQQYEIWRELFSPLHALNF
          Q.DSN.AAIPH..EDIQGD.RW.SQH.....LD.KDK...VLFV.D.MVQLMQQ.EIWRELFS.LH....
Retrocopy QADSNAAAIPHTVEDIQGDNRWISQHNRFV-LDGKDKKPNVLFVEDPMVQLMQQHEIWRELFSLLHR---

Parental  GIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVKLI--NTRQPQAKIIVLGL
          G...DT.RHVL..L.N.ELENIK.KVI.V.VGT.NHEN...E..G.I.AI...I...T..........GL
Retrocopy GSKEDT-RHVL*KLRNRELENIKLKVIAV*VGTDNHENAVKELEGEIKAIIHFISLSTQDSHKSNSSIGL

Parental  L-PRGEKPNPLRQKNAKVNQLLKVSLPKLANVQLLDADGGFVHSDGAISCHDMFDFLHLTGGGYAKICKP
          ..PRGEKPNPLRQK...VNQLLKVS..KL..V..L..D.GF.H.D.AISCHD.FDFL.LTG.GY.KI.K.
Retrocopy V>PRGEKPNPLRQK---VNQLLKVSPLKLSHV*VLHTDRGFMHQDSAISCHDIFDFLQLTG*GYPKIYKA

Parental  LHELIMQLLEETPEEKHTTIA
          L.ELIMQL.EETP.EK.T.IA
Retrocopy LGELIMQLMEETPTEKQTIIA

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	14.33 RPM
SRP051959_heart	0.00 RPM	13.49 RPM
SRP051959_kidney	0.07 RPM	12.89 RPM
SRP051959_liver	0.00 RPM	7.93 RPM
SRP051959_lung	0.05 RPM	13.39 RPM
SRP051959_lymph_node	0.00 RPM	12.24 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.94 RPM
SRP051959_spleen	0.00 RPM	11.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3325 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3325 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1148
Pan troglodytes	retro_ptro_782
Gorilla gorilla	retro_ggor_893
Pongo abelii	retro_pabe_953
Macaca mulatta	retro_mmul_892

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325 ,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,