RetrogeneDB ID: retro_cjac_1690

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:41584390..41585210(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMNAT1
• Ensembl ID: ENSCJAG00000005483
• Aliases: None
• Description: nicotinamide nucleotide adenylyltransferase 1 [Source:HGNC Symbol;Acc:17877]

Sequence

>retro_cjac_1690
ATAGAAAATTCAAAGAAGACTGAAGTGGTTCTCTTTGCTCGTGGTTCCTTTAATCCTGTCACCAACATACACCTCAGGTT
GTTTGAGCTGGCCAAGGACGTCGTGAGTGGAACAGGATGATATAGAGTTGTCAAAGACATAATCTCTCCTGTTGGCAATG
CATACCAGGAGAAAGGATTCATTCCTGCCCATGGCCGGGTCATCATGTCAGAACTTGCCACCAAGAAGTCCAAATGGTTG
GAAGCTGGAAATGGAATGGGAAAGTCTTCAGAGTGGATAGAGACTGGTAAGGTGCTAATACACCACCAAGAGAAACTAGG
GGCTAGTAACTGTGATAATCAGCAGAACTTCCGATGCTAGAAAGGCCTGGACAAAAGAGGAAGTGGACTGAACAAAGGCA
AGATTCTAGTTAAAAGAAATCCCTAGAGCCCAAAAGAAAAGGTGCAACAAGGTCAAGCTATTGTGTGGGACAGATTTACC
AGAGTCCTTTGACGTTCCCAGTGTGTGGAAGAGCGAAGACATCCCCCAAATCATGGCAGACTATGAGCTCGCATGTATTA
CTCGGGCTGGAAATGACGCTCAGAAATTCATCCATGAATCTGATGTGTTGTGAAAATACCTGAGCTACGTTCATGTAGTG
AACGAATGCATTACTAATGATATTTCATCTACAAAAACCCAGAGAGCCCTCAGAAGGGGCCAGAACATTTGCTACTTGAT
GCGAGAACTTGTCCAAGAATACACCGAAAAGCATAATTCGTTCAGCGCCGAGAGTGAAGACAGGAAGACTGGGATCATTC
TGGCCCCTTTGCAGAAACAC

Alignment

ORF - retro_cjac_1690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.01 %
• Parental protein coverage: 97.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MENSEETEVVLLACGSFNPITNMHLRLFELAKDYLNGTGRYRVVKGIISPVGDAYKKKGLIPAHHRVIMA
          .ENS..TEVVL.A.GSFNP.TN.HLRLFELAKD...GTG.YRVVK.IISPVG.AY..KG.IPAH.RVIM.
Retrocopy IENSKKTEVVLFARGSFNPVTNIHLRLFELAKDVVSGTG*YRVVKDIISPVGNAYQEKGFIPAHGRVIMS

Parental  ELATKNSKWVEVDTWESLQKEWKETLKVLRHHQEKLEASNCDHQQNS-PTLERPGRKRKWTEQKQDSNQK
          ELATK.SKW.E.........EW.ET.KVL.HHQEKL.ASNCD.QQN..P.LERPG.KRKWTEQ.QDS..K
Retrocopy ELATKKSKWLEAGNGMGKSSEWIETGKVLIHHQEKLGASNCDNQQNF<PMLERPGQKRKWTEQRQDSS*K

Parental  KSLDPKTKAAP-KVKLLCGADLLESFAVPNLWKSEDIAQIVADYGLICVTRAGNDAQKFIYESDVLWKHR
          KSL.PK.K.A..KVKLLCG.DL.ESF.VP..WKSEDI.QI.ADY.L.C.TRAGNDAQKFI.ESDVL.K..
Retrocopy KSLEPKRKGAT<KVKLLCGTDLPESFDVPSVWKSEDIPQIMADYELACITRAGNDAQKFIHESDVL*KYL

Parental  SNIHVVNEWITNDISSTKIRRALRRGQSIRYLVPDLVQEYIENHNLYSSESEDRNAGVILAPLQRN
          S..HVVNE.ITNDISSTK..RALRRGQ.I.YL...LVQEY.E.HN..S.ESEDR..G.ILAPLQ..
Retrocopy SYVHVVNECITNDISSTKTQRALRRGQNICYLMRELVQEYTEKHNSFSAESEDRKTGIILAPLQKH

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	0.04 RPM	2.26 RPM
SRP051959_heart	0.00 RPM	1.63 RPM
SRP051959_kidney	0.04 RPM	2.22 RPM
SRP051959_liver	0.00 RPM	1.17 RPM
SRP051959_lung	0.02 RPM	1.30 RPM
SRP051959_lymph_node	0.00 RPM	1.03 RPM
SRP051959_skeletal_muscle	0.02 RPM	2.58 RPM
SRP051959_spleen	0.02 RPM	1.28 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1690 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1690 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1690 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_247
Macaca mulatta	retro_mmul_446

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001361	2 retrocopies	retro_btau_1153, retro_btau_1654,
Callithrix jacchus	ENSCJAG00000005483	1 retrocopy	retro_cjac_1690 ,
Homo sapiens	ENSG00000173614	3 retrocopies	retro_hsap_247, retro_hsap_2740, retro_hsap_2989,
Macaca mulatta	ENSMMUG00000005863	2 retrocopies	retro_mmul_1488, retro_mmul_446,
Nomascus leucogenys	ENSNLEG00000009375	2 retrocopies	retro_nleu_1072, retro_nleu_741,
Oryctolagus cuniculus	ENSOCUG00000023212	1 retrocopy	retro_ocun_1243,
Otolemur garnettii	ENSOGAG00000033037	2 retrocopies	retro_ogar_1088, retro_ogar_637,