RetrogeneDB ID: retro_cjac_545

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:73595944..73596809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010077
• Aliases: None
• Description: None

Sequence

>retro_cjac_545
ATGGTTTCAATCCCAGAATACTATGAAGGCAAGAATGTCCTCCTCACAGGAGCTACTGGTTTTCTAGGGAAGGTGCTTTC
TGGAAAAGTTGCTGAGATCTTGTCCTAAGGTGAATTCAGTGTATGTTTTGGTGAGGCAGAAAGCTAGACAGACACCACAA
GAGCGAGTAGAAGAAATCCTTAGTGGCAAGCTCTTTGACAGACTGAGAGATGAAAATCCAGATTTTAGAGAGAAAATTAT
AGCAATCGACAGCGAACTCACCCAACCTAAACTGGCTCTCAGTGAAGAAGATAAAGAGGTGATCATAGATTCTACCAATA
TTATATTCCACTGTGCAGCTACAGTAAGGTTTAATGAAAACTTAAGAGATGCTGTTCAGGTAAGTGCGATTGCAATGCGA
CAGCTTATTCTCCTTGCACAACAAATGAAGAATCTGGAGGTATTCATGCATGTATCAACAGCATGTGCCTGCTGTAACCG
AAAGCATATTGATGAAGTAGTCTACCCACCACCTGTGGATCCCAAGAAGCTGACTGATTCTTTAGAGTGGATGGATGATG
GCCTAGTAAATGATATCACACCAAAATTGATAGGAGACAGACCTAATACCTACATATACACAAAAGCATTGGCAGAATAT
GTTGTACAACAGGAAGGAGCAAAGCTAAATGTGGCGATTATAAGGCTATCGATTGTTGGTGCCAGTTGGAAAGAACTTTT
TCCAGGATGGATTGATAATTTTAATGGACCAAGTGGGCTCTTTATTGCAGCAGGGAAAGGAATTCTTCAAAAAATGCATG
CCTCCAACAGGGCCCTTGCAGATCTTGTTCCTGTAGACGTAGTTGTCAACGAGTCTTGCAGCAGC

Alignment

ORF - retro_cjac_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.43 %
• Parental protein coverage: 55.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVSIPEYYEGKNVLLTGATGFLGKVL-LEKLLRSCPKVNSVYVLVRQKARQTPQERVEEILSGKLFDRLR
          MVSIPEYYEGKNVLLTGATGFLGKVL.LEKLLRSCPKVNSVYVLVRQKARQTPQERVEEILSGKLFDRLR
Retrocopy MVSIPEYYEGKNVLLTGATGFLGKVL>LEKLLRSCPKVNSVYVLVRQKARQTPQERVEEILSGKLFDRLR

Parental  DENPDFREKIIAINSELTQPKLALSEEDKEVIIDSTNIIFHCAATVRFNENLRDAVQLNVIATRQLILLA
          DENPDFREKIIAI.SELTQPKLALSEEDKEVIIDSTNIIFHCAATVRFNENLRDAVQ...IA.RQLILLA
Retrocopy DENPDFREKIIAIDSELTQPKLALSEEDKEVIIDSTNIIFHCAATVRFNENLRDAVQVSAIAMRQLILLA

Parental  QQMKNLEVFMHVSTAYAYCNRKHIDEVVYPPPVDPKKLIDSLEWMDDGLVNDITPKLIGDRPNTYIYTKA
          QQMKNLEVFMHVSTA.A.CNRKHIDEVVYPPPVDPKKL.DSLEWMDDGLVNDITPKLIGDRPNTYIYTKA
Retrocopy QQMKNLEVFMHVSTACACCNRKHIDEVVYPPPVDPKKLTDSLEWMDDGLVNDITPKLIGDRPNTYIYTKA

Parental  LAEYVVQQEGAKLNVAIIRPSIVGASWKEPFPGWIDNFNGPSGLFIAAGKGILRTMRASNSALADLVPVD
          LAEYVVQQEGAKLNVAIIR.SIVGASWKE.FPGWIDNFNGPSGLFIAAGKGIL..M.ASN.ALADLVPVD
Retrocopy LAEYVVQQEGAKLNVAIIRLSIVGASWKELFPGWIDNFNGPSGLFIAAGKGILQKMHASNRALADLVPVD

Parental  VVVNMSLAA
          VVVN.S...
Retrocopy VVVNESCSS

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	0.02 RPM	23.72 RPM
SRP051959_heart	0.04 RPM	24.92 RPM
SRP051959_kidney	0.00 RPM	23.12 RPM
SRP051959_liver	0.00 RPM	5.26 RPM
SRP051959_lung	0.00 RPM	25.08 RPM
SRP051959_lymph_node	0.02 RPM	26.32 RPM
SRP051959_skeletal_muscle	0.00 RPM	11.14 RPM
SRP051959_spleen	0.06 RPM	41.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_545 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_545 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003490	2 retrocopies	retro_chof_1358, retro_chof_1733,
Callithrix jacchus	ENSCJAG00000010077	1 retrocopy	retro_cjac_545 ,
Cavia porcellus	ENSCPOG00000002654	1 retrocopy	retro_cpor_267,
Homo sapiens	ENSG00000197601	1 retrocopy	retro_hsap_1225,
Gorilla gorilla	ENSGGOG00000001180	1 retrocopy	retro_ggor_958,
Macaca mulatta	ENSMMUG00000011990	1 retrocopy	retro_mmul_1301,
Nomascus leucogenys	ENSNLEG00000017695	1 retrocopy	retro_nleu_698,
Oryctolagus cuniculus	ENSOCUG00000004336	2 retrocopies	retro_ocun_1056, retro_ocun_790,
Otolemur garnettii	ENSOGAG00000005064	2 retrocopies	retro_ogar_1353, retro_ogar_341,
Pongo abelii	ENSPPYG00000003470	1 retrocopy	retro_pabe_1019,
Pan troglodytes	ENSPTRG00000024190	1 retrocopy	retro_ptro_840,
Rattus norvegicus	ENSRNOG00000013176	1 retrocopy	retro_rnor_467,