RetrogeneDB ID: retro_cjac_1425

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:87467894..87468677(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHX
• Ensembl ID: ENSCJAG00000010888
• Aliases: None
• Description: pyruvate dehydrogenase complex, component X [Source:HGNC Symbol;Acc:21350]

Sequence

>retro_cjac_1425
ATTGGTTTGATAGAAGAAGAAGATTGGAAACACGTTGAAATTCCCAAAGATGTAGGTCCTCCACCACCAGCTTCAAAACC
TTCAGAGCCTCGTCCCTCACCAGAACCACAGATTGCCATCCCTGTCAAGAAGGAACACACACCCAGGATACTACAGTTCC
GTTTAAGGCCAGCTGCCTGCAATATTCTGGAAGAACACTCACTGGATGCTAACCAGGGCACAGCCAATGGTCCTCGGGGG
ATATTCACAAAAGAGGATGCTCTCAGACTTGCCCAGTTGAAACAGATGGTGGCCAAGATTACCGAGTCCAGATCAACCCC
AGCCCCTGCAGCCACTCCCACAGCACCTTCACCCCTACAGGCCATAACCGGGCCATCTTATCCCCGGCTTATGATCCCAC
CAGCATCCACTCCTGGACAACCCAATGCAGTGGGCACATTCACTGAAATCCCCGCCAGCAATATTCCAAGAGTTATTGCC
AAGAGATTAACTGAATCGAAAAGTACTGTACCTCATGCGTATGCTACTGCTGACTTTGACCTTGGAGCTGTTTTAAAAGT
TAGGCAAGATCTGGTCAAAGGTGACATTAGAGTATCAGTAAATGATTTTATCATCAAGGCAGCAGCTGTTACCCTTAAAC
AAATGCCAGATGTTAAAGTGAGCTGGGATGGAGAGGGCCCAAAGCAACTGCCATGTGTTGACATTTCAGTGGCCGAGGCA
ACAGATAAAGGCTTCATTACACCAGTCATTAAGGATGCTGCTGCTAAGGGTATCCAGGCTCTG

Alignment

ORF - retro_cjac_1425 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.17 %
• Parental protein coverage: 52.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGLIVEEGEDWKHVEIPKDVGPPPPPSKPSEPRPSPEPQVAIPVKKEHTPGTLQFRLSPAARNILEKHSL
          IGLI.EE..DWKHVEIPKDVGPPPP.SKPSEPRPSPEPQ.AIPVKKEHTP..LQFRL.PAA.NILE.HSL
Retrocopy IGLIEEE--DWKHVEIPKDVGPPPPASKPSEPRPSPEPQIAIPVKKEHTPRILQFRLRPAACNILEEHSL

Parental  DASQGTATGPRGIFTKEDALRLAQLKQM-GKITESRPAPAPAATPTAPSPLQATAGPSYPRPMIPPVSTP
          DA.QGTA.GPRGIFTKEDALRLAQLKQM..KITESR..PAPAATPTAPSPLQA..GPSYPR.MIPP.STP
Retrocopy DANQGTANGPRGIFTKEDALRLAQLKQMVAKITESRSTPAPAATPTAPSPLQAITGPSYPRLMIPPASTP

Parental  GQPFAVGTFTEIPASNIRRVIAKRLTESKSTVPHAYATADCDLGAVLKVRQDLVKDDIKVSVNDFIIKAA
          GQP.AVGTFTEIPASNI.RVIAKRLTESKSTVPHAYATAD.DLGAVLKVRQDLVK.DI.VSVNDFIIKAA
Retrocopy GQPNAVGTFTEIPASNIPRVIAKRLTESKSTVPHAYATADFDLGAVLKVRQDLVKGDIRVSVNDFIIKAA

Parental  AVTLKFLKNILVSWDGEAPKQLPCIDISVV-ATDKGLITPIIKDAAAKGIQEI
          AVTLK......VSWDGE.PKQLPC.DISV..ATDKG.ITP.IKDAAAKGIQ..
Retrocopy AVTLKQMPDVKVSWDGEGPKQLPCVDISVAEATDKGFITPVIKDAAAKGIQAL

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	0.24 RPM	12.03 RPM
SRP051959_heart	0.63 RPM	31.15 RPM
SRP051959_kidney	0.31 RPM	19.50 RPM
SRP051959_liver	0.43 RPM	15.57 RPM
SRP051959_lung	0.29 RPM	15.16 RPM
SRP051959_lymph_node	0.09 RPM	9.82 RPM
SRP051959_skeletal_muscle	0.70 RPM	28.17 RPM
SRP051959_spleen	0.17 RPM	12.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1425 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1425 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
Choloepus hoffmanni	ENSCHOG00000003998	1 retrocopy	retro_chof_2128,
Callithrix jacchus	ENSCJAG00000010888	1 retrocopy	retro_cjac_1425 ,
Mus musculus	ENSMUSG00000010914	1 retrocopy	retro_mmus_2937,