RetrogeneDB ID: retro_ptro_1491

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:38443088..38443670(+)
• Located in intron of: ENSPTRG00000014402

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM54A
• Ensembl ID: ENSPTRG00000018634
• Aliases: None
• Description: None

Sequence

>retro_ptro_1491
GAATATTCTGGTGTTCCTATAGATCAGGTTTTGCTGATTTGGGAAAATAAAGGCTATGGATCAACTAGGAATACTGTTCA
TATTAATGAGGAAATGCTTCTGTTAGAACCTTGTTGAAGGCACAATTTTGAGTTGATCCAGTTCTTGAACTCTGTAGACT
CTGACAATTCTGGATCTATTGTTTCATCTTTTGCTGATATTTTGTGTGTGGCAAATGTTGAGGAAGCCAGTTTTCTCAGA
TTTCAAAATAGTATATGGAAAAATGAAGAGAAAATGGAATGTGTCCATCCTTTGCAACTAGTTTGGGATCCAGTGTCATC
TGCTCTAAAACACAACAAACCAGTGAAAAATGATCTGCTTGTAAATGAAGCTACAATTAAAAAAAAAATAGGTGCCCTTG
AAGATGAGCTAACTTTTCTTCACTCTCAGATTCCTGCAATTTTGGAAATGCAGGAATTGAAAAACAGTACAAATTCTAGT
TCCTTTGGCTTGAATGATGGGCCCATTAGTTTGGGACAAATGCCATCATCAGGGGCTGTTCAGCTGAGTGGGGAGGCACA
CATATATATTTGTTCTTTACTA

Alignment

ORF - retro_ptro_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 50.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EYFGVPVEQVLLIWENKDYGSTRSIVRIIGKMLPLEPCRRPNFELIPLLNSVDSDNCGSMVPSFADILYV
          EY.GVP..QVLLIWENK.YGSTR..V.I...ML.LEPC.R.NFELI..LNSVDSDN.GS.V.SFADIL.V
Retrocopy EYSGVPIDQVLLIWENKGYGSTRNTVHINEEMLLLEPC*RHNFELIQFLNSVDSDNSGSIVSSFADILCV

Parental  ANDEEASYLRFRNSIWKNEEEKVEIFHPLRLVRDPLSPAVRQKETVKNDLPVNEATI-RKIAALENELTF
          AN.EEAS.LRF.NSIWKN.EEK.E..HPL.LV.DP.S.A......VKNDL.VNEATI.....ALE.ELTF
Retrocopy ANVEEASFLRFQNSIWKN-EEKMECVHPLQLVWDPVSSALKHNKPVKNDLLVNEATIXXXXGALEDELTF

Parental  LRSQIAAIVEMQELKNSTNSSSFGLSDEHISLGQLSSSRAAHPSVEPDRFPGSVL
          L.SQI.AI.EMQELKNSTNSSSFGL.D..ISLGQ..SS.A...S.E......S.L
Retrocopy LHSQIPAILEMQELKNSTNSSSFGLNDGPISLGQMPSSGAVQLSGEAHIYICSLL

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	0.00 RPM	0.30 RPM
SRP007412_cerebellum	0.00 RPM	1.08 RPM
SRP007412_heart	0.00 RPM	0.15 RPM
SRP007412_kidney	0.00 RPM	0.86 RPM
SRP007412_liver	0.00 RPM	0.88 RPM
SRP007412_testis	0.00 RPM	10.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1491 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1491 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000244	1 retrocopy	retro_cfam_1178,
Myotis lucifugus	ENSMLUG00000002331	1 retrocopy	retro_mluc_2227,
Monodelphis domestica	ENSMODG00000017453	1 retrocopy	retro_mdom_1813,
Nomascus leucogenys	ENSNLEG00000014793	1 retrocopy	retro_nleu_1513,
Pan troglodytes	ENSPTRG00000018634	1 retrocopy	retro_ptro_1491 ,