RetrogeneDB ID: retro_ptro_604

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:47174741..47175213(-)
• Located in intron of: ENSPTRG00000003555

Retrocopy information

• Ensembl ID: ENSPTRG00000041905
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ASNA1
• Ensembl ID: ENSPTRG00000010537
• Aliases: None
• Description: ATPase ASNA1 [Source:UniProtKB/TrEMBL;Acc:K6ZIZ2]

Sequence

>retro_ptro_604
CAGATCAAGAACCAGATCAGCCCCTTTATCTTACAGACATGCAACATTCTAGGTCTTGGGGACATGAACACAGACGTGCT
GTCCTCCATGCTGAAGTAGACACTGTCCATCATCTACTTTGTCAGCAAACAGTTCAAGGGCCCTGAGTAGATTACCTGTA
TCATCTGCGAATGTATCCCTGAGTTCTATCCCTGTATGAGACAGAGTGACTGATCCAGGAGCTGGCCAAGTACAAGATTG
ACACATACAACATCATCATCACCCAGCTTCTCTTCCCCAACCCTGAAAATCCTGAAAGATATGTGAGGCCTGACACAAGA
TCCAGGCCAAGTATCTGAACCAGATGGAGAACCCTTATAAAGACTTTTGCACTGTGAAACTGCCACTGTTTCCCCATGAG
GTGCAGGGGGCAGACAAAGTCAACACGTTCTCAGCCCTCTTTATGGAACCCTACAAGCCCTGTAGCACCCAG

Alignment

ORF - retro_ptro_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.25 %
• Parental protein coverage: 53.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QIKNQISPFISQMCNMLGLGDMNADQLASKLEETLPVIRSVSEQFKDPE-QTTFICVCIAEF-LSLYETE
          QIKNQISPFI.Q.CN.LGLGDMN.D.L.S.L..TL..I..VS.QFK.PE..T..IC.CI.EF.LSLYETE
Retrocopy QIKNQISPFILQTCNILGLGDMNTDVLSSMLK*TLSIIYFVSKQFKGPE*ITCIICECIPEF<LSLYETE

Parental  RLIQELAKCKIDTHNIIVNQLVFPDPEKPC-KMCEARHKIQAKYLDQMEDLYEDFHIVKLPLLPHEVRGA
          .LIQELAK.KIDT.NII..QL.FP.PE.P..K.CEA.HKIQAKYL.QME..Y.DF..VKLPL.PHEV.GA
Retrocopy *LIQELAKYKIDTYNIIITQLLFPNPENPE<KICEA*HKIQAKYLNQMENPYKDFCTVKLPLFPHEVQGA

Parental  DKVNTFSALLLEPYKPPSAQ
          DKVNTFSAL..EPYKP.S.Q
Retrocopy DKVNTFSALFMEPYKPCSTQ

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
SRP007412_brain_prefrontal_cortex	0.02 RPM	51.00 RPM
SRP007412_cerebellum	0.04 RPM	64.20 RPM
SRP007412_heart	0.06 RPM	27.66 RPM
SRP007412_kidney	0.00 RPM	79.14 RPM
SRP007412_liver	0.00 RPM	45.40 RPM
SRP007412_testis	0.00 RPM	71.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_604 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005010	1 retrocopy	retro_etel_656,
Nomascus leucogenys	ENSNLEG00000010460	1 retrocopy	retro_nleu_2842,
Otolemur garnettii	ENSOGAG00000012205	1 retrocopy	retro_ogar_931,
Pan troglodytes	ENSPTRG00000010537	1 retrocopy	retro_ptro_604 ,