RetrogeneDB ID: retro_cjac_1106

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:66314811..66315720(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARIH2
• Ensembl ID: ENSCJAG00000003305
• Aliases: None
• Description: None

Sequence

>retro_cjac_1106
ATGTTCCTGGACATGAATAGCCACTGGTCTGACAGCAGTAAAGAAAACTATGATCCAAGTTGTAAAGAAGAGGGTGAAGA
CCCTAGGGACATAGAGGATTATTACACGGCAGTAGCCAGCAATGTGGGACAGCAGGGGGCTGATGCCTTTGATCTGGCGG
AGTACCAGTTCACTTGCTTGACCTACAAGGAATGTGAAGGTGCCCTCAAATGAGCACATGGCCAGCTTAGCCTCTGTCCT
AAAGGTATTTCATTCAGTCGCTAAACTTATATTAGTTAATTTCCACTGGCAAGTTTCAGAGATATTGGACAGATACAAGT
CCAATTCTGTTCAACTGCTCGTTGAGGCTCGAGTTCAGCCTAATCCCTTTAAACGTGTTCCCACTTCCCATCCTCCTCAC
CACTGTGCAATGTGTATGCAGTTTGTGTAAAAAGAAAACCTACTCTCTCTGGCCTTTTAGCATCAGATTTGCCGCAGCTG
CTGGGAGCAGCACTGCTTAGTTCTCGTCAAGGACGGCGTGGGCGAGGGAGTCTCTTGTATGGCTCAGACTGTCCACTCCA
TACACAAGAGGACTTTGTGTTTCCATTGCTTCCCAGTGAAGAATTGAGAGAGAAATACAGGTGCTACCTCTTCAGGGACC
ATGTGGAGAGTCATTACCAGCTCCAGCTGTGCCCTGGTGCAGACTGCCCCATGATTATTTGGGTACAGGAGCCTAGAGCT
CTCTGAGTACAGTGCAATTGGTGCAAGGAGGTCTTCTGTTTCAAGTGTCATCAGATGTATCAAACATCCACAGACTGCAT
CACAATCTAGAAATGGCTCAAAAAGTGTGCAGACAACTCTGGAACAGCCAACTACATTAGTGCTCACACTAAAGATGGCC
CCAAGTGCAACATCAGGCTGCAATCACAT

Alignment

ORF - retro_cjac_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVDMNSQGSDSNEEDYDPNCEEEEEEDEDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESEG
          M..DMNS..SDS..E.YDP.C....EE.EDP.DIEDYY..VAS.V.QQGADAFD..EYQFTCLTYKE.EG
Retrocopy MFLDMNSHWSDSSKENYDPSCK---EEGEDPRDIEDYYTAVASNVGQQGADAFDLAEYQFTCLTYKECEG

Parental  AL-NEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVSTSHPPHHCA
          AL.NEHM.SLASVLKV.HSVAKLILVNFHWQVSEILDRYKSNS.QLLVEARVQPNP.K.V.TSHPPHHCA
Retrocopy AL>NEHMASLASVLKVFHSVAKLILVNFHWQVSEILDRYKSNSVQLLVEARVQPNPFKRVPTSHPPHHCA

Parental  VCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQ-DCPLRTPEDFVFPLLPNEELREK
          .CMQFV.KENLLSLA..HQ.CRSCWEQHC.VLVKDGVG.GVSCMAQ.DCPL.T.EDFVFPLLP.EELREK
Retrocopy MCMQFV*KENLLSLAF*HQICRSCWEQHCLVLVKDGVGEGVSCMAQ<DCPLHTQEDFVFPLLPSEELREK

Parental  YRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTK
          YR.YLFRD.VESHYQLQLCPGADCPM.I.VQEPRA..VQCN.C.EVFCFKC.QMY...TDC.TI.KWL.K
Retrocopy YRCYLFRDHVESHYQLQLCPGADCPMIIWVQEPRAL*VQCNWCKEVFCFKCHQMYQTSTDCITI*KWLKK

Parental  CADDSETANYISAHTKDCPKCNICIEKN
          CAD.S.TANYISAHTKD.PKCNI.....
Retrocopy CADNSGTANYISAHTKDGPKCNIRLQSH

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	21.85 RPM
SRP051959_heart	0.00 RPM	41.08 RPM
SRP051959_kidney	0.02 RPM	29.37 RPM
SRP051959_liver	0.00 RPM	23.09 RPM
SRP051959_lung	0.00 RPM	36.73 RPM
SRP051959_lymph_node	0.00 RPM	36.73 RPM
SRP051959_skeletal_muscle	0.00 RPM	45.40 RPM
SRP051959_spleen	0.00 RPM	31.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1106 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1106 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1876
Pan troglodytes	retro_ptro_1259
Gorilla gorilla	retro_ggor_1373
Pongo abelii	retro_pabe_1557

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013035	1 retrocopy	retro_amel_1021,
Callithrix jacchus	ENSCJAG00000003305	1 retrocopy	retro_cjac_1106 ,
Homo sapiens	ENSG00000177479	1 retrocopy	retro_hsap_1876,
Gorilla gorilla	ENSGGOG00000017134	1 retrocopy	retro_ggor_1373,
Myotis lucifugus	ENSMLUG00000013946	1 retrocopy	retro_mluc_1869,
Mustela putorius furo	ENSMPUG00000014344	1 retrocopy	retro_mputfur_610,
Mus musculus	ENSMUSG00000064145	1 retrocopy	retro_mmus_795,
Nomascus leucogenys	ENSNLEG00000006710	1 retrocopy	retro_nleu_1228,
Oryctolagus cuniculus	ENSOCUG00000017699	1 retrocopy	retro_ocun_1838,
Pongo abelii	ENSPPYG00000013890	1 retrocopy	retro_pabe_1557,
Pan troglodytes	ENSPTRG00000014902	1 retrocopy	retro_ptro_1259,
Ictidomys tridecemlineatus	ENSSTOG00000001766	1 retrocopy	retro_itri_1047,