RetrogeneDB ID: retro_cjac_2973

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:45035373..45035912(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABHD10
• Ensembl ID: ENSCJAG00000020230
• Aliases: None
• Description: abhydrolase domain containing 10 [Source:HGNC Symbol;Acc:25656]

Sequence

>retro_cjac_2973
GTACCTTGTCGGAGCTGGAGCTGGGCAGCTGTCCCCTTCGTTCCCTACCAGGGCCTCAACATGCTGTTTGCACCAAAGCC
TCAGTGGGTGCCATGGTGGCCCCCAGCTTGCAGACAAAAGACATCATTCTCTTTCCTTAATTGACCAGACCCTCCAAACC
TGGCTTTTAAGAGGCTAAAAGGCAAAAGTCCAGGAATTTTATCTTCATCCCTGGCTATATTTCTAATATGAATGGTACAA
AAGCATTGGCGATTGAGTTTTGCGAATCTCTAAGTCACACCTACATAAGGTTTGATTACTCAGGAGTTAGAAGTTCAGAC
AGTAACCTGGAGGCAAGCACACTGGGGAAATGGAGGAAAGATGATCTTTCTATAATTGATGACTTAGCTGAAGGGCCACA
GATTCATGCTGGATCTAGCCTCAGGTGGTGGCTTAAGCTTCATGCTGCAATTGCACGACCAGAAAAGGTTATGGCTCTTA
TTGGTGTATCTACAGCTGCAGATGGCTTAGTGACACAGTTTAATCAGCTTCCTGTTGAG

Alignment

ORF - retro_cjac_2973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.4 %
• Parental protein coverage: 58.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPCRSWGWAAVAFGPHRGLNTLLAPMPRRAPRW-LPACRQKTSLSF--LNRPDLPKLAYKRLKGKSPGII
          VPCRSW.WAAV.F.P..GLN.L.AP.P...P.W..P....K....F..L.RP..P.........KS...I
Retrocopy VPCRSWSWAAVPFVPYQGLNMLFAPKPQWVPWW<APSLQTKDIILFP*LTRPSKPGF*EAK-RQKSRNFI

Parental  FIPGYISNMNGTKALAIEEFCKSLGHAYIRFDYSGVGSSDGNLEESTVGKWRKDVLSIIDDLAEGPQILV
          FIPGYISNMNGTKALAIE.FC.SL.H.YIRFDYSGV.SSD.NLE.ST.GKWRKD.LSIIDDLAEGPQI..
Retrocopy FIPGYISNMNGTKALAIE-FCESLSHTYIRFDYSGVRSSDSNLEASTLGKWRKDDLSIIDDLAEGPQIHA

Parental  GSSLGGWLMLHAAIARPEKVMALIGVAAAADGLVTRFNQLPVE
          GSSL..WL.LHAAIARPEKVMALIGV..AADGLVT.FNQLPVE
Retrocopy GSSLRWWLKLHAAIARPEKVMALIGVSTAADGLVTQFNQLPVE

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	0.11 RPM	2.55 RPM
SRP051959_heart	0.05 RPM	4.77 RPM
SRP051959_kidney	0.07 RPM	4.99 RPM
SRP051959_liver	0.04 RPM	5.00 RPM
SRP051959_lung	0.15 RPM	3.11 RPM
SRP051959_lymph_node	0.23 RPM	5.39 RPM
SRP051959_skeletal_muscle	0.02 RPM	5.70 RPM
SRP051959_spleen	0.08 RPM	3.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2973 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2973 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020230	1 retrocopy	retro_cjac_2973 ,
Cavia porcellus	ENSCPOG00000005650	1 retrocopy	retro_cpor_1498,
Dipodomys ordii	ENSDORG00000014818	1 retrocopy	retro_dord_28,
Felis catus	ENSFCAG00000029739	1 retrocopy	retro_fcat_176,
Ochotona princeps	ENSOPRG00000009517	1 retrocopy	retro_opri_1051,
Tursiops truncatus	ENSTTRG00000016358	1 retrocopy	retro_ttru_778,