RetrogeneDB ID: retro_cjac_1506

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:33649200..33649751(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPA2
• Ensembl ID: ENSCJAG00000005448
• Aliases: None
• Description: non imprinted in Prader-Willi/Angelman syndrome 2 [Source:HGNC Symbol;Acc:17044]

Sequence

>retro_cjac_1506
ATGAGCCAGGGGTGTGGAAATACGACTTTTATATTGGTCTGGGATTGGCTATGAGCGCCAGCATTTTCATTGAAGGAAGT
TTGATTTGGGGCAGGAAAAAGGATTCTGCGATTTGCCATAGAAGGCACCAGGAGACCAGGTCAAGGTGGCCACGCAAATC
CTAAAGAATGATTGTAGTAGGCTGGACTGCTGTCAACGGGAGTTGGCGAGGTGGCCAACTTACCTGCATGTGGGTTTGCA
CCGGCCACACTGGTGACTTCACCAAGACCTCTCAGCATTCTAGTAAGTGCCATTCTTTCTTCATACTTTCTAAAAAAAGA
TAGAATCTTTATGGGAAAATTGGTTGTTTGGCAAGTATTTGAGGATCTACAGTTATGATCACTCATCCTCCAAACAAAGA
GGATATCGAAACTAACTAAAATATCTCACAGCTAGGTGATCCAGGTTTCATGGACTTTGCAACACTTGTGATCATAATGG
CCATGATATTAATCTTCCTGTTGGGTCCCCACCATGGACAATAATCTTGTGTATGTAACAATCTGCTCTGT

Alignment

ORF - retro_cjac_1506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.3 %
• Parental protein coverage: 51.39 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSQGRG-KYDFYIGLGLAMSSSIFIGGSFILKKKG-LLRLARKGSMRAGQGGHAYLKEWLWWAGLLSMGA
          MSQG.G.KYDFYIGLGLAMS.SIFI.GS.I...K...LR.A..G..R.GQGGHA..KE.L..AGLLS.G.
Retrocopy MSQGCG<KYDFYIGLGLAMSASIFIEGSLIWGRKK>ILRFAIEGTRRPGQGGHANPKE*L**AGLLSTGV

Parental  GEVANFAAYAFAPATLVTPLGALSVLVSAILSSYFL-NERLNLHGKIGCLLSILGSTVMVIHAPKEEEIE
          GEVAN..A..FAPATLVT....LS.LVSAILSSYFL...R.NL.GKIGCL.SI.GSTVM..H.P..E.IE
Retrocopy GEVANLPACGFAPATLVTSPRPLSILVSAILSSYFL<KKR*NLYGKIGCLASI*GSTVMITHPPNKEDIE

Parental  TLDEMSHKLGDPGFVVFATLVVIVALILIFVVGPRHGQTNILVYITIC
          T....S..LGDPGF..FATLV.I.A.ILIF..GP.HGQ.........C
Retrocopy TN*NIS-QLGDPGFMDFATLVIIMAMILIFLLGPHHGQ*SCVCNNLLC

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	26.11 RPM
SRP051959_heart	0.00 RPM	12.02 RPM
SRP051959_kidney	0.00 RPM	24.32 RPM
SRP051959_liver	0.00 RPM	11.94 RPM
SRP051959_lung	0.21 RPM	20.38 RPM
SRP051959_lymph_node	0.00 RPM	30.62 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.47 RPM
SRP051959_spleen	0.00 RPM	21.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1506 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1506 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506 ,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,