RetrogeneDB ID: retro_cjac_3139

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:59045067..59045535(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NCBP2
• Ensembl ID: ENSCJAG00000013735
• Aliases: None
• Description: nuclear cap binding protein subunit 2, 20kDa [Source:HGNC Symbol;Acc:7659]

Sequence

>retro_cjac_3139
ATGTCCAGTGGCCTACTGAAGGCGCTGTGCAGCGACACCTACCTGGAGCTGAGCCAGTACCAGGACTAGCATTTCCAGAG
TGACAATGAAAATCAAGAAAAATTACTGAAGAAAAGCTGTATGTTATAGGTTGGAAATCTTTCTTTTTACACAACTGAAG
AACAAATCTATGAACTTTCAGCAAAAGTGGTAACATAAAGAAAATCATTATGGGTCTAGATAAAATGAAGAAAACAGCAT
GTGAGTTCTGTTTCGTGGAGTATTACTCACGAGCAGATGCAAAAAAATGCTGTGCAATACATAAATGGAACTCGTCTGGA
TGACTGAATCATTCACACAGATTGGGACGCAGGCTTTAAGGAGGGCAGGCAGTATGGCCGTGGGCGATCTTGGGGCCAGG
TACAGGATGTGTATAGGCAGGACTATGATGATGGGAGAGGAAGCTATGGAAAACTGGCACAGGACCAG

Alignment

ORF - retro_cjac_3139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYEL-FSKSGDIKKI
          MS.GLLKAL.SD.Y.ELSQY.D.HF..DNE.QEKLLKKSC.L.VGNLSFYTTEEQIYEL.FSKSG.IKKI
Retrocopy MSSGLLKALCSDTYLELSQYQD*HFQSDNENQEKLLKKSCML*VGNLSFYTTEEQIYEL<FSKSGNIKKI

Parental  IMGLDKMKKTACGFCFVEYYSRADA-ENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEY
          IMGLDKMKKTAC.FCFVEYYSRADA..NA..YINGTRLDD.II.TDWDAGFKEGRQYGRGRS.GQV.D.Y
Retrocopy IMGLDKMKKTACEFCFVEYYSRADA>KNAVQYINGTRLDD*IIHTDWDAGFKEGRQYGRGRSWGQVQDVY

Parental  RQDYDAGRGGYGKLAQNQ
          RQDYD.GRG.YGKLAQ.Q
Retrocopy RQDYDDGRGSYGKLAQDQ

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	15.80 RPM
SRP051959_heart	0.02 RPM	24.38 RPM
SRP051959_kidney	0.00 RPM	25.71 RPM
SRP051959_liver	0.00 RPM	15.70 RPM
SRP051959_lung	0.00 RPM	26.60 RPM
SRP051959_lymph_node	0.00 RPM	34.18 RPM
SRP051959_skeletal_muscle	0.04 RPM	25.44 RPM
SRP051959_spleen	0.00 RPM	34.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3139 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3139 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003664	2 retrocopies	retro_amel_113, retro_amel_62,
Bos taurus	ENSBTAG00000008873	1 retrocopy	retro_btau_1819,
Canis familiaris	ENSCAFG00000013100	2 retrocopies	retro_cfam_152, retro_cfam_2195,
Callithrix jacchus	ENSCJAG00000013735	2 retrocopies	retro_cjac_3139 , retro_cjac_4103,
Cavia porcellus	ENSCPOG00000002976	1 retrocopy	retro_cpor_611,
Equus caballus	ENSECAG00000016153	1 retrocopy	retro_ecab_79,
Felis catus	ENSFCAG00000029865	2 retrocopies	retro_fcat_1936, retro_fcat_561,
Homo sapiens	ENSG00000114503	1 retrocopy	retro_hsap_5,
Loxodonta africana	ENSLAFG00000006372	1 retrocopy	retro_lafr_129,
Macropus eugenii	ENSMEUG00000004730	1 retrocopy	retro_meug_34,
Microcebus murinus	ENSMICG00000003162	1 retrocopy	retro_mmur_488,
Myotis lucifugus	ENSMLUG00000017500	2 retrocopies	retro_mluc_355, retro_mluc_592,
Mustela putorius furo	ENSMPUG00000003806	1 retrocopy	retro_mputfur_9,
Mus musculus	ENSMUSG00000022774	2 retrocopies	retro_mmus_2381, retro_mmus_2645,
Nomascus leucogenys	ENSNLEG00000001727	1 retrocopy	retro_nleu_1239,
Oryctolagus cuniculus	ENSOCUG00000006738	2 retrocopies	retro_ocun_1887, retro_ocun_833,
Otolemur garnettii	ENSOGAG00000005009	6 retrocopies	retro_ogar_3151, retro_ogar_3152, retro_ogar_3153, retro_ogar_3160, retro_ogar_3161, retro_ogar_3162,
Pongo abelii	ENSPPYG00000014449	1 retrocopy	retro_pabe_85,
Pan troglodytes	ENSPTRG00000015789	1 retrocopy	retro_ptro_3151,
Pteropus vampyrus	ENSPVAG00000017273	3 retrocopies	retro_pvam_238, retro_pvam_305, retro_pvam_939,
Sarcophilus harrisii	ENSSHAG00000004363	2 retrocopies	retro_shar_161, retro_shar_46,
Tupaia belangeri	ENSTBEG00000015222	3 retrocopies	retro_tbel_2153, retro_tbel_3367, retro_tbel_758,
Tarsius syrichta	ENSTSYG00000014263	1 retrocopy	retro_tsyr_2008,
Tursiops truncatus	ENSTTRG00000013908	2 retrocopies	retro_ttru_442, retro_ttru_826,
Vicugna pacos	ENSVPAG00000010369	1 retrocopy	retro_vpac_493,