RetrogeneDB ID: retro_cjac_3117

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:24131471..24132562(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSCJAG00000001585
• Aliases: None
• Description: None

Sequence

>retro_cjac_3117
TTCAAGTTGACAAACTTTCCAGAAATGATGAATAGATATAAACAGCTATTGACCTATATTCAGAGTGCTGTCACAAGAAA
TTATTCTGAAAAATTCATTAATTCTATTCTTGATTATATCTCTACTTCTAAACAGATGGATTTACTGCAGAAATTCTATG
AAACAACTCTGGAAGTTTGAAAGATGCTAAGAATGATAGACTGTGGTTTAAGACAAACACAAAACTTGGAAAATTATATT
TAGAACGAGAGGAGTATGGAAAACTTCAAAAAATTTTACACCAGTTATATCAGTCCTGCCAGACTGATGATGGAGAAGAT
GGTCTGAAAAAGGGTGCACAGTTATTAGAAAATATATGCTTTGGAAATTCAGATGTACACAGCACAGAAAAATAACAAAA
AATCTAAAGCACTCTATGAACAGTCACTTCACATCAAGTCTGCCATCCCTCATCCACTGATCATGGGAGTTATCAGAGAA
TGTGGTGGTAAAATGCACTTGAGAGAAGGTGAATTTGAAAAGGCACACACTAATTTTTTTGAAGCCTTCAAGAATTATGA
TGAATCTGGAAATCTGAGACTAACTACTTGCTTAAAATATTTGGTCTTAGCAAATATGCTTATGAAATCAGGAATAAATC
CATTTGACTCACAGGAGGCAAAGCCGTACAAAAATGATCCAGAAATTTTAGCAATGACAAATTTAGTAAATGCCTATCAG
AATAATGACATCACTGAATTTGAAAAGATTCTAAAAACAAATCACAGCAACATCATGGATGATCCTTTTATAAGAGAACA
CATTGAAGAGGTTTTGTGAAACATCAGAGCACAAGTGCTTATAAAATTAATTAAACCTTACACAAGAATACATATTCCTT
TTATTTCTAAGGAATTAAACATAGATGTAGCGATGTGGAGAGCTTGCTGGTGCAGTGCATATTGGATAACACTATTCATG
GCTGAATTGATCAAGTCAACCAGCTCCTTGAACTGGATCATCAGAAGAGGAGTGGTGCACGATATACTGCACTAGATCAA
TGGACCAACCAACTAAATTCTCTCAACCAGGCTGTAGTCAGTAAACTGGCT

Alignment

ORF - retro_cjac_3117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.19 %
• Parental protein coverage: 96.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YDLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYISTSKQMDLLQEFYETTLE-ALKDAKNDRLW
          ..LTNFPEMMNRYKQLLTYI.SAVTRNYSEK.INSILDYISTSKQMDLLQ.FYETTLE..LKDAKNDRLW
Retrocopy FKLTNFPEMMNRYKQLLTYIQSAVTRNYSEKFINSILDYISTSKQMDLLQKFYETTLE<SLKDAKNDRLW

Parental  FKTNTKLGKLYLEREEYGKLQKILRQLHQSCQTDDGEDDLKKGTQLLE-IYALEIQMYTAQKNNKKLKAL
          FKTNTKLGKLYLEREEYGKLQKIL.QL.QSCQTDDGED.LKKG.QLLE.IYALEIQMYTAQKNNKK.KAL
Retrocopy FKTNTKLGKLYLEREEYGKLQKILHQLYQSCQTDDGEDGLKKGAQLLE>IYALEIQMYTAQKNNKKSKAL

Parental  YEQSLHIKSAIPHPLIMGVIRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLM
          YEQSLHIKSAIPHPLIMGVIRECGGKMHLREGEFEKAHT.FFEAFKNYDESG..R.TTCLKYLVLANMLM
Retrocopy YEQSLHIKSAIPHPLIMGVIRECGGKMHLREGEFEKAHTNFFEAFKNYDESGNLRLTTCLKYLVLANMLM

Parental  KSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQ
          KSGINPFDSQEAKPYKNDPEILAMTNLV.AYQNNDITEFEKILKTNHSNIMDDPFIREHIEE.L.NIR.Q
Retrocopy KSGINPFDSQEAKPYKNDPEILAMTNLVNAYQNNDITEFEKILKTNHSNIMDDPFIREHIEEVL*NIRAQ

Parental  VLIKLIKPYTRIHIPFISKELNIDVA-DVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGARYTALDK
          VLIKLIKPYTRIHIPFISKELNIDVA.DVESLLVQCILDNTIHG.IDQVNQLLELDHQKR.GARYTALD.
Retrocopy VLIKLIKPYTRIHIPFISKELNIDVA<DVESLLVQCILDNTIHG*IDQVNQLLELDHQKRSGARYTALDQ

Parental  WTNQLNSLNQAVVSKLA
          WTNQLNSLNQAVVSKLA
Retrocopy WTNQLNSLNQAVVSKLA

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	24.52 RPM
SRP051959_heart	0.05 RPM	38.33 RPM
SRP051959_kidney	0.02 RPM	33.39 RPM
SRP051959_liver	0.02 RPM	28.61 RPM
SRP051959_lung	0.02 RPM	33.67 RPM
SRP051959_lymph_node	0.02 RPM	28.90 RPM
SRP051959_skeletal_muscle	0.04 RPM	42.15 RPM
SRP051959_spleen	0.02 RPM	34.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3117 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3117 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013425	1 retrocopy	retro_btau_452,
Choloepus hoffmanni	ENSCHOG00000013375	7 retrocopies	retro_chof_1083, retro_chof_1288, retro_chof_2209, retro_chof_2371, retro_chof_2520, retro_chof_2550, retro_chof_678,
Callithrix jacchus	ENSCJAG00000001585	2 retrocopies	retro_cjac_3105, retro_cjac_3117 ,
Callithrix jacchus	ENSCJAG00000014450	1 retrocopy	retro_cjac_4166,
Echinops telfairi	ENSETEG00000019523	2 retrocopies	retro_etel_2160, retro_etel_88,
Macaca mulatta	ENSMMUG00000009838	1 retrocopy	retro_mmul_62,
Monodelphis domestica	ENSMODG00000002466	1 retrocopy	retro_mdom_891,
Oryctolagus cuniculus	ENSOCUG00000006455	1 retrocopy	retro_ocun_1296,
Otolemur garnettii	ENSOGAG00000013284	1 retrocopy	retro_ogar_1513,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497,
Tursiops truncatus	ENSTTRG00000000462	1 retrocopy	retro_ttru_328,