RetrogeneDB ID: retro_cjac_2819

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:78712507..78712945(-)
• Located in intron of: ENSCJAG00000012158

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC57
• Ensembl ID: ENSCJAG00000002991
• Aliases: None
• Description: leucine rich repeat containing 57 [Source:HGNC Symbol;Acc:26719]

Sequence

>retro_cjac_2819
AAACTAGAGATGCTATACCTAAAGGGCAGTCATCTGAGAGAGCTGCCATCTACGTTTGGGCAACTGTCTATCCTCAAGAC
CCTGAGCCTCACTGGGAACCAACTGGGAGAACTATCACCCAACTTTGTGCCTAGGGCACCAGATGTGGCAGATATTTCCA
AGAACCAGATTCAAAGTATACCTGATAACTAAGACAGCTGCAGGTCATCAAACTCAACCTCAACCAGAAGCAGATATCTC
AGGTCTCAATAGAGATATCTTGCTGTCCTTGCCTTAAAAGTATTCACCTGGGAGAGCTCAGCATGCTTTCACAAAGCATC
TGCAGTGATTATCAGATCTGTTCCCTTGCTGTGGAAGGTAATCCTTTTTGAAGTAAAGAAACTTCAAGAATTTGAAGCCT
ATGATAAGTACATGGAGAGGTTCATGGCCGCCAAGAAG

Alignment

ORF - retro_cjac_2819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.63 %
• Parental protein coverage: 63.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLETLSLNNNHLRELPSTFGQLSALKTLSLSGNQLGALPPQLCTLRHLDVVDLSKNQIRSIPDT-VGQLQ
          KLE.L.L...HLRELPSTFGQLS.LKTLSL.GNQLG.L.P.....R..DV.D.SKNQI.SIPD....QLQ
Retrocopy KLEMLYLKGSHLRELPSTFGQLSILKTLSLTGNQLGELSPNFVP-RAPDVADISKNQIQSIPDN<LRQLQ

Parental  VIELNLNQNQISQISVKISCCPRLKILRLEENCLELSMLPQSILSDSQICLLAVEGN-LFEIKKLRELEG
          VI.LNLNQ.QISQ.S..ISCCP.LK...L.E....LSML.QSI.SD.QIC.LAVEGN.LFE.KKL.E.E.
Retrocopy VIKLNLNQKQISQVSIEISCCPCLKSIHLGE----LSMLSQSICSDYQICSLAVEGN>LFEVKKLQEFEA

Parental  YDKYMERFTATKK
          YDKYMERF.A.KK
Retrocopy YDKYMERFMAAKK

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	1.86 RPM
SRP051959_heart	0.02 RPM	3.23 RPM
SRP051959_kidney	0.00 RPM	2.55 RPM
SRP051959_liver	0.00 RPM	1.45 RPM
SRP051959_lung	0.00 RPM	4.28 RPM
SRP051959_lymph_node	0.00 RPM	2.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.34 RPM
SRP051959_spleen	0.02 RPM	2.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2819 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2819 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2819 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2163
Pan troglodytes	retro_ptro_1650
Gorilla gorilla	retro_ggor_1718

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819 ,
Callithrix jacchus	ENSCJAG00000016965	1 retrocopy	retro_cjac_2430,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027, retro_lafr_767,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,