RetrogeneDB ID: retro_cjac_2446

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:60846009..60846470(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019556
• Aliases: None
• Description: None

Sequence

>retro_cjac_2446
TTCCAAAAAATGACCACAACCTCTTCAGTAGAAGATAAACAGAATCTAGTATTTATGAGTAGGAAGACCTGGTTTTCAAT
TACTGAAAATAATTGATCTTTAAAGTACAGAATTAATTTAGTTCTCAGTAGAGAACTCAAGAAACCACCACAAGAGCTAA
TTTTCTTGCCTAAAGTCTGGGTGATGTCTTAAAACTTACTGGGCAACGAGAATTAACAAACAAACTGGACATGGTTTTCA
AAGGGGGAGGCAGTTCTGTTTGGAAGAAAGCCATGAATTAAGACACCATTTTAAACTATTTGAGACATGGATCATGCAGG
ACTTTGAAAGTGGCACTTTTTCCCCCGGAAGTTGATTTAGAGAAATAGAAACTTCTCCCAGAATACCCACAACATATTGT
CTCTGATGTGAAAGAGGAGAAAAGCGTTAAGTACAAATTTGAAGTATATTAAAAGAATGAT

Alignment

ORF - retro_cjac_2446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.24 %
• Parental protein coverage: 81.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FQRMTTTSSVEDKQNLVIMGRKTWFSIPEKNRPLKDRINVVLSREL-KEPPQ-GALLARSLDDALKLTEQ
          FQ.MTTTSSVEDKQNLV.M.RKTWFSI.E.N..LK.RIN.VLSREL.K.P......LA.SL.D.LKLT.Q
Retrocopy FQKMTTTSSVEDKQNLVFMSRKTWFSITENN*SLKYRINLVLSRELKKPPQE<ANFLA*SLGDVLKLTGQ

Parental  PELANKVDMIWIIGGSSVYKEAM-DHPGHLKLFVTRIMQDFESDTFFP-EIDLEKYKLLPQYPG-VPSDD
          .EL.NK.DM....GGSSV.K.AM.....H.KLF.T.IMQDFES.TF.P.E.DLEK.KLLP.YP....SD.
Retrocopy RELTNKLDMVFKGGGSSVWKKAM<ELRHHFKLFETWIMQDFESGTFSP>EVDLEK*KLLPEYPQHIVSDV

Parental  QEEKGIKYKFEVYEKND
          .EEK..KYKFEVY.KND
Retrocopy KEEKSVKYKFEVY*KND

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	5.66 RPM
SRP051959_heart	0.07 RPM	2.82 RPM
SRP051959_kidney	0.00 RPM	11.20 RPM
SRP051959_liver	0.00 RPM	34.90 RPM
SRP051959_lung	0.00 RPM	2.29 RPM
SRP051959_lymph_node	0.00 RPM	2.83 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.12 RPM
SRP051959_spleen	0.00 RPM	2.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2446 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2446 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2446 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3602
Pan troglodytes	retro_ptro_2988
Gorilla gorilla	retro_ggor_2429

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015750	2 retrocopies	retro_amel_218, retro_amel_842,
Bos taurus	ENSBTAG00000007681	1 retrocopy	retro_btau_351,
Callithrix jacchus	ENSCJAG00000019556	4 retrocopies	retro_cjac_2017, retro_cjac_2298, retro_cjac_2446 , retro_cjac_531,
Equus caballus	ENSECAG00000026827	1 retrocopy	retro_ecab_513,
Felis catus	ENSFCAG00000026745	3 retrocopies	retro_fcat_579, retro_fcat_705, retro_fcat_841,
Homo sapiens	ENSG00000228716	4 retrocopies	retro_hsap_1927, retro_hsap_2119, retro_hsap_3602, retro_hsap_6,
Gorilla gorilla	ENSGGOG00000022366	2 retrocopies	retro_ggor_1959, retro_ggor_2429,
Myotis lucifugus	ENSMLUG00000012200	2 retrocopies	retro_mluc_1109, retro_mluc_2577,
Macaca mulatta	ENSMMUG00000018283	13 retrocopies	retro_mmul_1496, retro_mmul_425, retro_mmul_692, retro_mmul_693, retro_mmul_695, retro_mmul_700, retro_mmul_701, retro_mmul_704, retro_mmul_738, retro_mmul_760, retro_mmul_768, retro_mmul_82, retro_mmul_994,
Monodelphis domestica	ENSMODG00000024860	3 retrocopies	retro_mdom_1685, retro_mdom_604, retro_mdom_703,
Mustela putorius furo	ENSMPUG00000008704	1 retrocopy	retro_mputfur_1107,
Mus musculus	ENSMUSG00000021707	1 retrocopy	retro_mmus_3326,
Nomascus leucogenys	ENSNLEG00000012989	3 retrocopies	retro_nleu_1193, retro_nleu_2314, retro_nleu_2631,
Oryctolagus cuniculus	ENSOCUG00000005127	3 retrocopies	retro_ocun_1351, retro_ocun_1640, retro_ocun_650,
Otolemur garnettii	ENSOGAG00000025320	1 retrocopy	retro_ogar_222,
Pongo abelii	ENSPPYG00000015600	2 retrocopies	retro_pabe_2959, retro_pabe_41,
Pan troglodytes	ENSPTRG00000017042	3 retrocopies	retro_ptro_109, retro_ptro_1551, retro_ptro_2988,
Rattus norvegicus	ENSRNOG00000013521	1 retrocopy	retro_rnor_2030,
Sus scrofa	ENSSSCG00000014125	2 retrocopies	retro_sscr_104, retro_sscr_1131,