RetrogeneDB ID: retro_cjac_2451

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:75086723..75087146(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A17
• Ensembl ID: ENSCJAG00000004636
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17 [Source:HGNC Symbol;Acc:10987]

Sequence

>retro_cjac_2451
ACAGTGCTTTTTCCCCTGGATACAGCTAGACTTCGACTTCAGGTTGACGAGAAAAGAAAATACAAAATTACACACATGGT
GCTCCTGGAGATCATTAAAAAGAAGGACTCTTGGCACTATATCGAGGGTGGTTTCCAGCGATTCTCAGTCTCTGCTGCTC
CAATTTTGTCTATTCCTACACTTCTAAAAGCCTCAAAGCAGTCTGGGTCAAAGGTCAACGTTCTACTACTGGAAAAGATC
TGGTAGTTGCTGTTTGTTGCAGGCGTGGTTAACACGTGGCTAACAACTCCACTCTGGGTGGTAAACACCAGAATGAAGCT
TCAAGGGGCAAAATTTAGGACTGAAGATTATACCGACAAACTACAAAGGTATCATGGATGCTTTGTATCAGATCATTCGA
GGTGAAGAAATCTTGGCTTGTTG

Alignment

ORF - retro_cjac_2451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.13 %
• Parental protein coverage: 53.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TVFFPLDTARLRLQVDEKRKSKTTHMVLLEIIKE-EGLLAPYRGWFPVISSLCCSNFVYFYTFNSLKAVW
          TV.FPLDTARLRLQVDEKRK.K.THMVLLEIIK..EGLLA.YRGWFP.I.SLCCSNFVY.YT..SLKAVW
Retrocopy TVLFPLDTARLRLQVDEKRKYKITHMVLLEIIKK<EGLLALYRGWFPAILSLCCSNFVYSYTSKSLKAVW

Parental  VKGQRSTTGKDLVIG-FVAGVVNVLLTTPLWVVNTRLKLQGAKFRNEDIVP--TNYKGIIDAFHQIIRDE
          VKGQRSTTGKDLV...FVAGVVN..LTTPLWVVNTR.KLQGAKFR.ED.......Y.G.....H...R..
Retrocopy VKGQRSTTGKDLVVA>FVAGVVNTWLTTPLWVVNTRMKLQGAKFRTEDYTDKLQRYHGCFVSDHSR*RNL

Parental  GIL
          G.L
Retrocopy GLL

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	3.53 RPM
SRP051959_heart	0.02 RPM	3.53 RPM
SRP051959_kidney	0.00 RPM	6.48 RPM
SRP051959_liver	0.00 RPM	4.05 RPM
SRP051959_lung	0.00 RPM	4.25 RPM
SRP051959_lymph_node	0.00 RPM	3.38 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.92 RPM
SRP051959_spleen	0.00 RPM	3.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2451 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2451 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2451 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004636	1 retrocopy	retro_cjac_2451 ,
Macaca mulatta	ENSMMUG00000008106	1 retrocopy	retro_mmul_453,
Monodelphis domestica	ENSMODG00000013036	1 retrocopy	retro_mdom_1808,