RetrogeneDB ID: retro_cjac_1331

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:32586514..32587388(+)
• Located in intron of: ENSCJAG00000010847

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSCJAG00000018128
• Aliases: CNN3, calponin-3
• Description: None

Sequence

>retro_cjac_1331
ATAGAAGAGGTAACAGGCATGAGCACTGGCACCAACTTCCAGCTGGGCTTAAAGGATGGTATCATACTCTGCAAACTCAT
AAACAAGCTACAGCCAGGCTCAGTGAAGGTCAACGAGTCTTCATTGAACTGGCCTCAGTTGGAGAATATTGGCAATTTTA
TTAAAGCTATTCAGGTTTATGGAATAGAGCCACATGACGTATTTGAAGCAAATGATCTTTTTGAGTATGGAAACATGACC
CAGGTTCAGAGACTTTAGTGGCTGTAGCAGGTCTGGCTAAAACAAAAGGATTCCATACAACCATTGACACTGGAGTTAAG
TATGCAGAAAAACAAACAAGATGTTTTGATGAAGGAAAATTAAAAGCTGGCCAAAGTGCAATTGGTCTGCAGATGGGAAC
CAACAAATGTGCCAGCCAGCAGGTATGACAGCTTATGGGACTAGGAGGCATCTTTATGATCCCAAAATGCAAACTGACAA
ACCTTTTGACCAAACCGCAATTAGTCTGTAGATAGTCACTAACAAAGGAGCCAGCCCCACAGGGATGTTAGCACCAGGTA
CCAGGAGAGACATGTATGATCAGAAGCTAACATTACAGCCAGTGGACAACTCGAGAATTTCTCTACAGATGGGTACCAAC
AAAGTTGCTTCCCAGAAAGTAATGAGTGTGTAGGGGCTTGGGCAGCAAGTATATGATCCCAAATACTGTGCTGCTCCAAT
AGAACCTGTCATTCACAATGGAAGCCAAGGAACAGGAACAAATGGTTCAGTAATCAGTGACAGCGATTATCAGGCAGAAT
ACCCTGATGAGTATCATGGCAAGTACCAGGATGACTACCCCAGAGATTACCCATATAGTGACCAAGCCATTGAT

Alignment

ORF - retro_cjac_1331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.75 %
• Parental protein coverage: 89.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IEEVTGMSIGTNFQLGLKDGIILCELINKLQPGSVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFE
          IEEVTGMS.GTNFQLGLKDGIILC.LINKLQPGSVK.VNESSLNWPQLENIGNFIKAIQ.YG..PHD.FE
Retrocopy IEEVTGMSTGTNFQLGLKDGIILCKLINKLQPGSVK-VNESSLNWPQLENIGNFIKAIQVYGIEPHDVFE

Parental  ANDLFENGNMTQVQT-TLVALAGLAKTKGFHTTIDIGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCA
          ANDLFE.GNMTQVQ..TLVA.AGLAKTKGFHTTID.GVKYAEKQTR.FDEGKLKAGQS.IGLQMGTNKCA
Retrocopy ANDLFEYGNMTQVQR<TLVAVAGLAKTKGFHTTIDTGVKYAEKQTRCFDEGKLKAGQSAIGLQMGTNKCA

Parental  SQ-AGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTI
          SQ.AGMTAYGTRRHLYDPKMQTDKPFDQT.ISL...TNKGAS..GMLAPGTRRD.YDQKLTLQPVDNS.I
Retrocopy SQ<AGMTAYGTRRHLYDPKMQTDKPFDQTAISL*IVTNKGASPTGMLAPGTRRDMYDQKLTLQPVDNSRI

Parental  SLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEPVIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYQ
          SLQMGTNKVASQK.MSV.GLG.QVYDPKYCAAP.EPVIHNGSQGTGTNGS.ISDSD..............
Retrocopy SLQMGTNKVASQKVMSV*GLGQQVYDPKYCAAPIEPVIHNGSQGTGTNGSVISDSDXXXXXXXXXXXXXX

Parental  DDYPRDYPYSDQGID
          ..YPRDYPYSDQ.ID
Retrocopy XXYPRDYPYSDQAID

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	0.93 RPM	59.60 RPM
SRP051959_heart	1.40 RPM	62.71 RPM
SRP051959_kidney	1.51 RPM	140.53 RPM
SRP051959_liver	0.91 RPM	66.80 RPM
SRP051959_lung	2.13 RPM	71.95 RPM
SRP051959_lymph_node	3.47 RPM	18.10 RPM
SRP051959_skeletal_muscle	0.48 RPM	17.10 RPM
SRP051959_spleen	2.21 RPM	36.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1331 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1331 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1331 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000005530	1 retrocopy	retro_cjac_681,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Callithrix jacchus	ENSCJAG00000012755	2 retrocopies	retro_cjac_723, retro_cjac_778,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331 , retro_cjac_533, retro_cjac_861,
Dasypus novemcinctus	ENSDNOG00000012883	3 retrocopies	retro_dnov_223, retro_dnov_403, retro_dnov_815,
Equus caballus	ENSECAG00000020188	1 retrocopy	retro_ecab_655,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mustela putorius furo	ENSMPUG00000003332	1 retrocopy	retro_mputfur_896,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sorex araneus	ENSSARG00000012874	1 retrocopy	retro_sara_582,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Tarsius syrichta	ENSTSYG00000010749	2 retrocopies	retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,