RetrogeneDB ID: retro_cjac_3936

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286328.1:2804..3275(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLA2G12A
• Ensembl ID: ENSCJAG00000016169
• Aliases: None
• Description: phospholipase A2, group XIIA [Source:HGNC Symbol;Acc:18554]

Sequence

>retro_cjac_3936
ATGGCCCTGCTCCCGCGCCCCGCACTCATCCTCCTGATCCTCCTCACGGGCCGCTGTTGTCAGGTGCCAGGAGCAGGCCC
AGACCACCGACTGGAGGGCCACCCTGAAGATCATCCGGAACGGCGTTCACAAGATACACACGTACCTGAACGCCGCCTTG
GACCTCCTGGGAGGCGAGGACGGTCTCTGCCAGTATGAATGCAGTGGCGGATCTAAGCCTTTCCACGTTGTGGTTACAGA
CCCTCCACACCGAATGGAAGTGCCTCTCCACTGTTTGGTGTTCATCTTAACATGGAGATCCCCTCCCTGACAAAAAGCTG
CAACCAACACCATAGGTGCTAGGAGACCTGTGGCAAAAGCAAGAATGACTGCGACGAGGAATTCCAATATTGCCTCTCCA
GGATCTGCCGAGATGTACTCAGCGTGTTCAGGCCTGTGAAACAGCAGTGGAGCTCTTGTTTGACAGCGTTA

Alignment

ORF - retro_cjac_3936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.25 %
• Parental protein coverage: 82.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALLPLPALILL-LLT-AAVVRCQEQAQTTDWRATLKTIRNGVHKIDTYLNAALDLLGGEDGLCQYKCSD
          MALLP.PALILL.LLT.AAVVRCQEQAQTTDWRATLK.IRNGVHKI.TYLNAALDLLGGEDGLCQY.CS.
Retrocopy MALLPRPALILLILLT>AAVVRCQEQAQTTDWRATLKIIRNGVHKIHTYLNAALDLLGGEDGLCQYECSG

Parental  GSKPF-PRYGYKPSPPNGCGSPLFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRD
          GSKPF.PR.GY.PS.PNG..SPLFGVHLN..IPSLTK.CNQH.RC.ETCGKSKNDCDEEFQYCLS.ICRD
Retrocopy GSKPF<PRCGYRPSTPNGSASPLFGVHLNMEIPSLTKSCNQHHRC*ETCGKSKNDCDEEFQYCLSRICRD

Parental  VQKTL-GLTQHVQACETAV
          V........Q....C.TA.
Retrocopy VLSVFRPVKQQWSSCLTAL

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	13.58 RPM
SRP051959_heart	0.00 RPM	21.43 RPM
SRP051959_kidney	0.00 RPM	31.22 RPM
SRP051959_liver	0.00 RPM	18.58 RPM
SRP051959_lung	0.00 RPM	21.15 RPM
SRP051959_lymph_node	0.00 RPM	22.44 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.31 RPM
SRP051959_spleen	0.00 RPM	20.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3936 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3936 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936 ,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172, retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,