RetrogeneDB ID: retro_cjac_4196

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:84159379..84160230(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000018334
• Aliases: None
• Description: None

Sequence

>retro_cjac_4196
ATGTCTGGGGACGAAATGATTTTTGATCCTACCATAAGCAAGAAGAAAAAGAAGAAGAAGCCTTTTATGTTAGATGAGGA
AGGGGATACCCAAACAGAGGAAACCTAGCCTTCAGAAACAAAAGAAGTGGAGCCAGAGCCAACTGAGGACAAAGATTTGG
AAGCTGATGAAGAGGACAGTAGGAAAAAACATGCTTCTGATGATGTAGATGACTTGAACTTATTTAATCAAAATAAAAGG
AAGAAAAAAACTAAAAAGATATTTGATATTGATGAAGCTGAAGAAGGTGTAAAGGATCTTAAGATTGAAAGTGATGTTCA
AGAACCTGCTGAACCAGAGGATGACCTGACATTAAGCTTGGCAATAAAAAGAAAAAGAAGAATGTCAAGTTCCCAGATTA
GGATGAAATACTAGAGAAAGATGAAGCTCTAGAAGATGAAGACCTCAAAAAAGATGATGGCATCTCAGTCAGTAATCAGA
CAGGCCCTGCTTGGGCAGGCTCAGAAAGAGACTACACATATGAGGAGCTGCTGAATTGAGTGTTCAACATCATGAGGGAA
AAGAATCCAGATATGGTTGCTGGGGAGAAAAGGAAATTTGTCATGAAACCTCCACAGGTCGTCCGAGTAGGAACCAAGAA
AACTTCTTTTGTCAACTTTACAGATATCTGTAAACGATTACATCGTCAGCCCAAACATCTCCTTGCATTTTCGTTGGCTG
AATTGGGTACAAGTGGTTCTATAGATGGTAATAACCAAATTGTAATCAAAGGAAGATTCCAACAGAAACATAGAAAATGT
CTTGAGAAGATATATCAAAGAATATGTCACTTGTCACACATGCCGATCACC

Alignment

ORF - retro_cjac_4196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.24 %
• Parental protein coverage: 86.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGDEMIFDPTMSKKKKKKKKPFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEEDSRKKDASDDL
          MSGDEMIFDPT.SKKKKKKK.PFMLDEEGDTQTEET.PSETKEVEPEPTEDKDLEADEEDSRKK.ASDD.
Retrocopy MSGDEMIFDPTISKKKKKKK-PFMLDEEGDTQTEET*PSETKEVEPEPTEDKDLEADEEDSRKKHASDDV

Parental  DDLNFFNQKKKKKKTKKIFDIDEAEEGVKDLKIESDVQEPAEPEDDL-DIMLGNKKKKKKNVKFPDEDEI
          DDLN.FNQ.K.KKKTKKIFDIDEAEEGVKDLKIESDVQEPAEPEDDL.DI.LGNKKKKK.NVKFPD.DEI
Retrocopy DDLNLFNQNKRKKKTKKIFDIDEAEEGVKDLKIESDVQEPAEPEDDL<DIKLGNKKKKK-NVKFPD*DEI

Parental  LEKDEALEDEDSKKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQV
          LEKDEALEDED.KKDDGIS.SNQTGPAWAGSERDYTYEELLN.VFNIMREKNPDMVAGEKRKFVMKPPQV
Retrocopy LEKDEALEDEDLKKDDGISVSNQTGPAWAGSERDYTYEELLN*VFNIMREKNPDMVAGEKRKFVMKPPQV

Parental  VRVGTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYV
          VRVGTKKTSFVNFTDICK.LHRQPKHLLAF.LAELGTSGSIDGNNQ.VIKGRFQQK........Y.....
Retrocopy VRVGTKKTSFVNFTDICKRLHRQPKHLLAFSLAELGTSGSIDGNNQIVIKGRFQQKHRKCLEKIYQR---

Parental  TCHTCRSPDT
          .CH....P.T
Retrocopy ICHLSHMPIT

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	30.40 RPM
SRP051959_heart	0.00 RPM	31.71 RPM
SRP051959_kidney	0.07 RPM	27.67 RPM
SRP051959_liver	0.11 RPM	34.85 RPM
SRP051959_lung	0.02 RPM	29.20 RPM
SRP051959_lymph_node	0.00 RPM	31.94 RPM
SRP051959_skeletal_muscle	0.04 RPM	50.14 RPM
SRP051959_spleen	0.00 RPM	34.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4196 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4196 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271,
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196 , retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Homo sapiens	ENSG00000125977	3 retrocopies	retro_hsap_2176, retro_hsap_2260, retro_hsap_713,
Gorilla gorilla	ENSGGOG00000015546	5 retrocopies	retro_ggor_1683, retro_ggor_1726, retro_ggor_2007, retro_ggor_280, retro_ggor_604,
Microcebus murinus	ENSMICG00000006944	1 retrocopy	retro_mmur_1583,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
Macaca mulatta	ENSMMUG00000018095	1 retrocopy	retro_mmul_1483,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200,
Nomascus leucogenys	ENSNLEG00000010034	2 retrocopies	retro_nleu_2242, retro_nleu_466,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Pan troglodytes	ENSPTRG00000013412	2 retrocopies	retro_ptro_1600, retro_ptro_508,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508,