RetrogeneDB ID: retro_cjac_3891

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285907.1:3902..4588(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENO1
• Ensembl ID: ENSCJAG00000000359
• Aliases: None
• Description: None

Sequence

>retro_cjac_3891
AGGGAGGCCATGCGCATTGGGGATGAAGGTGGGTTTGCTCCCAACACCCTGGTGAATGAGGAAGGCCTGGAGCTGCTGAA
GACTTCGATTGGCAAAGCTGGTTACACCGATAAGATTGTTATCACCATGGACATAGCAGCCTCCAAGTTTTACAGGTTTG
GGAAGTATGTCCTGGACTTCAAGTCTTCTGATGACTCCAGCAGGTACATCTCACCTGACAAGCTGGCTGACCTGCACAAG
TTCTTCATCAATGACTACCCAGTGGTGTCTATGGAAAATCTCTTTGACCAGAATGACTGGGGAGCTTGGCAGAAGTTCAC
GGCCATTGCAGGAATCCAGGTGGTGGGGATAATCTCACAGTAACCAACCCGAAGAGGATTGCCAAGGCCACAGAGAAGTC
ATGCAACTGCCTCCTGCTCAGCGTGAACTAGATTGGCTCTGTGACCGAGTCCTTGCAGAGGTGCAAGCTGGCACAGGCCA
ATGGTTGGGGCGTCATGGTGTTGCATCATTCTGGGGAGACTGAACATACCTTCATTGCCTGCCTGGGGGTGGTGATGTGC
ACTGGGCAGACCAAGATGTGTGCCCCTTGCCAATAAGAGCGCTTGGCCAAGTAGAACCAGCTCCTCAGAATTGAAGAGGA
GCTGGGCAGCAACGCTAAATTTGCTGGCAGAAACTTCAGAAACCCC

Alignment

ORF - retro_cjac_3891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 53. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDATNVGDEGGFAPNILENKEGLELLKTAIGKAGYTDKVVIGMDVAASEFYRSGKYDLDFKSPDDPSRYI
          ..A...GDEGGFAPN.L.N.EGLELLKT.IGKAGYTDK.VI.MD.AAS.FYR.GKY.LDFKS.DD.SRYI
Retrocopy REAMRIGDEGGFAPNTLVNEEGLELLKTSIGKAGYTDKIVITMDIAASKFYRFGKYVLDFKSSDDSSRYI

Parental  SPDQLADLYKSFIKDYPVVSIEDPFDQDDWGAWQKFTASAGIQVV-GDDLTVTNPKRIAKAANEKSCNCL
          SPD.LADL.K.FI.DYPVVS.E..FDQ.DWGAWQKFTA.AGIQVV.GD.LTVTNPKRIAK.A.EKSCNCL
Retrocopy SPDKLADLHKFFINDYPVVSMENLFDQNDWGAWQKFTAIAGIQVV<GDNLTVTNPKRIAK-ATEKSCNCL

Parental  LLKVNQIGSVTESLQACKLAQANGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQL
          LL.VN.IGSVTESLQ.CKLAQANGWGVMV.H.SGETE.TFIA.L.V..CTGQ.K..APC..ERLAK.NQL
Retrocopy LLSVN*IGSVTESLQRCKLAQANGWGVMVLHHSGETEHTFIACLGVVMCTGQTKMCAPCQ*ERLAK*NQL

Parental  LRIEEELGSKAKFAGRNFRNP
          LRIEEELGS.AKFAGRNFRNP
Retrocopy LRIEEELGSNAKFAGRNFRNP

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	148.77 RPM
SRP051959_heart	0.00 RPM	85.02 RPM
SRP051959_kidney	0.00 RPM	148.18 RPM
SRP051959_liver	0.00 RPM	188.84 RPM
SRP051959_lung	0.00 RPM	50.46 RPM
SRP051959_lymph_node	0.00 RPM	86.37 RPM
SRP051959_skeletal_muscle	0.00 RPM	45.75 RPM
SRP051959_spleen	0.00 RPM	67.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3891 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3891 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891 , retro_cjac_438,
Callithrix jacchus	ENSCJAG00000011679	2 retrocopies	retro_cjac_115, retro_cjac_177,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Homo sapiens	ENSG00000074800	1 retrocopy	retro_hsap_325,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mustela putorius furo	ENSMPUG00000006382	2 retrocopies	retro_mputfur_1162, retro_mputfur_547,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Oryctolagus cuniculus	ENSOCUG00000010086	1 retrocopy	retro_ocun_933,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Ochotona princeps	ENSOPRG00000009492	1 retrocopy	retro_opri_969,
Pan troglodytes	ENSPTRG00000000109	1 retrocopy	retro_ptro_261,
Pteropus vampyrus	ENSPVAG00000005030	1 retrocopy	retro_pvam_317,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011,