RetrogeneDB ID: retro_cjac_3105

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:942348..943441(-)
• 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_3105
AACTTCAAGTTGACAAACTTTCCAGAAATGATGAATAGATATAAACAACTATTGACCTATATAGGAGTGCTGTCACAAGA
AATTATTCTGAAAAACCCATTAATTCTATTCTTGATTATATCTCTACTTCTAAATAGATGGATTTACTGCAGGAATTCTA
TGAAACAACTCTGGAAGCTTTGAAAGATGCTAAGAATGATAGACTGTGGTTTAAGACAAACACAAAGCTTGGAAAATTAT
ATTTAGAATGAGAGGAGTATGGAAAGCTTCAAAAAATGTTACGCCAGTGACATCAGTCCTGTCAGACTGATGATGGCGAA
GATGATCTGAAAAAGGGTACACAGTTATTAGAAATATATGCTCTGGAAATTCAAGTGTACACAGCACAGAAAAATAACAA
AAAACTTAAAGCACTCTATGAACAGTCACTTCACATCAAGTCTGCCATCCCTCATCCACTGATCATGGGAGTTCTCAGAG
AATGTGCTGGTAAAATGCACTTGAGGGAAGGTGAATTTGAAAAGGCACACACTGATTTTTTTGAAGCCTTCAAGAATTAT
GATGAATCTGGAAGTCCGAGATGAACTACTTGCTTAAAATATTTGGTCTTAGCAAATATGCTTATGAAATCAGGAATAAA
TCCATTTGACTCACAGGAGGCCAAGCCATACAAAAATGATCCAGAAATTTTAGCAATGACGAATTTAGTAAGTGCCTATC
AGAATAATGACATCACTGAATTTGAAAAGTTTTAAAAACAAATCACAGCAACATCATGGATGATCCTTTCATAAGAGAAC
ACATTGAAGAGCTTTTGCGAAACATCAGAGCACAAGTGCTTATAAAATTAATTAAACCTTACACAAGAATACATATTCCT
TATATTTCTAAGGAATTAAACATAGATGTAGCTGATGTGGAGAGCTTGCTGGTGCAGTGCATATTGGATAACACTATTCA
TGGCCGAATTGATCAAGTCAACCAGCTCCTTGAGCTGGATCATCAGCAGAGGGGTGGTGCACGATATCCTGCACTAGATC
AATGGACCAACCAACTAAATTCTCTCAACCAGGCTGTAGTCAGTACACTGGCT

Alignment

ORF - retro_cjac_3105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.28 %
• Parental protein coverage: 96.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DYDLTNFPEMMNRYKQLLTYI-RSAVTRNYSEKSINSILDYISTSKQMDLLQEFYETTLEALKDAKNDRL
          ...LTNFPEMMNRYKQLLTYI.RSAVTRNYSEK.INSILDYISTSK.MDLLQEFYETTLEALKDAKNDRL
Retrocopy NFKLTNFPEMMNRYKQLLTYI<RSAVTRNYSEKPINSILDYISTSK*MDLLQEFYETTLEALKDAKNDRL

Parental  WFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKAL
          WFKTNTKLGKLYLE.EEYGKLQK.LRQ.HQSCQTDDGEDDLKKGTQLLEIYALEIQ.YTAQKNNKKLKAL
Retrocopy WFKTNTKLGKLYLE*EEYGKLQKMLRQ*HQSCQTDDGEDDLKKGTQLLEIYALEIQVYTAQKNNKKLKAL

Parental  YEQSLHIKSAIPHPLIMGVIRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLM
          YEQSLHIKSAIPHPLIMGV.REC.GKMHLREGEFEKAHTDFFEAFKNYDESGSPR.TTCLKYLVLANMLM
Retrocopy YEQSLHIKSAIPHPLIMGVLRECAGKMHLREGEFEKAHTDFFEAFKNYDESGSPR*TTCLKYLVLANMLM

Parental  KSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEK-ILKTNHSNIMDDPFIREHIEELLRNIRT
          KSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEK..LKTNHSNIMDDPFIREHIEELLRNIR.
Retrocopy KSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEK<VLKTNHSNIMDDPFIREHIEELLRNIRA

Parental  QVLIKLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGARYTALDK
          QVLIKLIKPYTRIHIP.ISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQ.RGGARY.ALD.
Retrocopy QVLIKLIKPYTRIHIPYISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQQRGGARYPALDQ

Parental  WTNQLNSLNQAVVSKLA
          WTNQLNSLNQAVVS.LA
Retrocopy WTNQLNSLNQAVVSTLA

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	0.21 RPM	38.33 RPM
SRP051959_kidney	0.24 RPM	33.39 RPM
SRP051959_liver	0.09 RPM	28.61 RPM
SRP051959_lung	0.16 RPM	33.67 RPM
SRP051959_lymph_node	0.05 RPM	28.90 RPM
SRP051959_skeletal_muscle	0.09 RPM	42.15 RPM
SRP051959_spleen	0.11 RPM	34.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3105 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3105 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,