RetrogeneDB ID: retro_cjac_2145

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:68089655..68090261(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM248
• Ensembl ID: ENSCJAG00000004278
• Aliases: TMEM248, C2H7orf42
• Description: transmembrane protein 248 [Source:HGNC Symbol;Acc:25476]

Sequence

>retro_cjac_2145
ATTTTTAACATCCATGCCCTGGAGAATCTGAATGCATACATCATTGGTTGCCTCCCTTGGTGGTCTTTATGATCATTCTG
AGCACCATGGAATAGCTTTCCCAATTCTGGGCTGTTCATTCAAAATTGAGGAGATTACATCACCAGAAATGGCTGAAGAC
TGGAATACTTTTATGCTATGGTTTAATGATTTGGATTTGTGTCCATCAGAAAATGAAACACTAAGCCATCTCAAAAACAA
CACCAAAACTCTGGGGAGCATAATGACCATGTAGCCCAGAGCATCCACCAGCTTTCTCCACACCCTGGAGATTCAGGACC
AGTTAATATCTCAGTTGCAATCACCCTAACCCTGGACACACTCAAGTTCTTTGGAGGGTACTCTCATGGAATCACTCACC
AGTATTCAATCATTTTATGTCATCAGATTGGACTTTCAGCCAGAGAAGCTGACAAAGAGATAAATATTACCTTTACCCTG
CCTCCAGGTTAGAGATCAGATAGCTGTGCTCTTGAGAATCACCATGAGTAGATGGTGTTCACAGCCTGCATGACCCTCAG
AGACACCCTAGGTGTGTTCCCTGTCACTGTGCAGCCACCCTACTGT

Alignment

ORF - retro_cjac_2145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.15 %
• Parental protein coverage: 64.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFSINPLENLKVYISS-RPPLVVFMISVSAM-AIAFLTLGYFFKIKEIKSPEMAEDWNTFLLRFNDLDLC
          .F.I..LENL..YI....PPLVVFMI..S.M..IAF..LG..FKI.EI.SPEMAEDWNTF.L.FNDLDLC
Retrocopy IFNIHALENLNAYIIG<LPPLVVFMIILSTM<GIAFPILGCSFKIEEITSPEMAEDWNTFMLWFNDLDLC

Parental  VSENETLKHLTNDSTTPESTMTSGQARASTQSPQALE-DSGPVNISVAITLTLDPLKPFGGYSRNVTHLY
          .SENETL.HL.N...T..S.MT....RAST.....LE.DSGPVNISVAITLTLD.LK.FGGYS...TH.Y
Retrocopy PSENETLSHLKNNTKTLGSIMTM*P-RASTSFLHTLE<DSGPVNISVAITLTLDTLKFFGGYSHGITHQY

Parental  STILGHQIGLSGREAHEEINITFTLPTAWSSDDCALHGHCEQVVFTACMTLTASPGVFPVTVQPPHC
          S.IL.HQIGLS.REA..EINITFTLP....SD.CAL..H.E..VFTACMTL....GVFPVTVQPP.C
Retrocopy SIILCHQIGLSAREADKEINITFTLPPG*RSDSCALENHHE*MVFTACMTLRDTLGVFPVTVQPPYC

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	16.97 RPM
SRP051959_heart	0.00 RPM	18.35 RPM
SRP051959_kidney	0.00 RPM	25.69 RPM
SRP051959_liver	0.00 RPM	20.90 RPM
SRP051959_lung	0.00 RPM	27.96 RPM
SRP051959_lymph_node	0.00 RPM	19.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.77 RPM
SRP051959_spleen	0.00 RPM	21.41 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2145 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2145 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004278	1 retrocopy	retro_cjac_2145 ,
Cavia porcellus	ENSCPOG00000000830	1 retrocopy	retro_cpor_330,
Echinops telfairi	ENSETEG00000015971	1 retrocopy	retro_etel_2097,
Homo sapiens	ENSG00000106609	1 retrocopy	retro_hsap_3093,
Gorilla gorilla	ENSGGOG00000022776	1 retrocopy	retro_ggor_2124,
Myotis lucifugus	ENSMLUG00000000616	1 retrocopy	retro_mluc_1974,
Macaca mulatta	ENSMMUG00000015843	1 retrocopy	retro_mmul_1973,
Nomascus leucogenys	ENSNLEG00000013326	1 retrocopy	retro_nleu_2235,
Pan troglodytes	ENSPTRG00000019253	1 retrocopy	retro_ptro_2089,
Pteropus vampyrus	ENSPVAG00000002978	2 retrocopies	retro_pvam_988, retro_pvam_997,
Sorex araneus	ENSSARG00000001884	1 retrocopy	retro_sara_563,