RetrogeneDB ID: retro_cjac_2862

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:6591103..6591602(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38A
• Ensembl ID: ENSCJAG00000021594
• Aliases: None
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing A [Source:HGNC Symbol;Acc:25930]

Sequence

>retro_cjac_2862
ACCATAGAGTGAAGGATGCACATAGCATCCACTAACCCTCAGTATCTGGTGGAGAAGATCATTCAAAGACGAATCTACGA
GTCCAAGCACTGGGAAGAGGAACGCTTTGGACTTACAGCTGAACTTGTAGTTGATAAAGCCACAGAGTTAAGGTTTGTGG
GTGGCATCTGTGTTGGTAACATAAAATCAACACCATTTCTGTGTTTAATTTGAAGATGCTTCAAATTCAACCCAAGAAGC
ATGTCACTGTAGACTTTATAAAAAATGAAGATTTGAAGTATGCACACATGTTGGGGGCCCTTTCCGTGAGGCTGACGGGC
CCCGCAATTGATTGCTGCAAGTACTTGGAGACTTGGTGCAATGACTGTTGAAAAATCAAGAGCCAGAACTGAAATGGGGA
GTTTGAACTGATGTGTGTAGACGAGTTATTGATGCACTGTTGCCCAGTGAGCGAGTCTGTGATAGCGTTCTGCCCCGGCT
ACAGAAACGCTATGTATTA

Alignment

ORF - retro_cjac_2862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.37 %
• Parental protein coverage: 53.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TVKDAHSIHGTNPQYLVEKIIRTRIYESKYWKEECFGLTAELVVDKAMELRFVGGVYGGNIKPTPFLCL-
          T......I..TNPQYLVEKII..RIYESK.W.EE.FGLTAELVVDKA.ELRFVGG...GNIK.TPFLCL.
Retrocopy TIE*RMHIASTNPQYLVEKIIQRRIYESKHWEEERFGLTAELVVDKATELRFVGGICVGNIKSTPFLCL<

Parental  TLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTGTAIDCYKYLEPLYNDYRKIKSQNRNGEFELMH
          .LKMLQIQP.K...V.FIKNED.KY..MLGAL..RLTG.AIDC.KYLE...ND..KIKSQN.NGEFELM.
Retrocopy NLKMLQIQPKKHVTVDFIKNEDLKYAHMLGALSVRLTGPAIDCCKYLETWCNDC*KIKSQN*NGEFELMC

Parental  VDEF-IDELLHSERVCDIILPRLQKRYVL
          VDE..ID.LL.SERVCD..LPRLQKRYVL
Retrocopy VDEL<IDALLPSERVCDSVLPRLQKRYVL

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	9.43 RPM
SRP051959_heart	0.00 RPM	8.70 RPM
SRP051959_kidney	0.00 RPM	7.52 RPM
SRP051959_liver	0.00 RPM	6.52 RPM
SRP051959_lung	0.00 RPM	11.47 RPM
SRP051959_lymph_node	0.02 RPM	12.15 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.95 RPM
SRP051959_spleen	0.02 RPM	11.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2862 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2862 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
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862 ,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,