RetrogeneDB ID: retro_ptro_852

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:19082587..19083502(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASC4
• Ensembl ID: ENSPTRG00000007010
• Aliases: None
• Description: None

Sequence

>retro_ptro_852
GAGCTTCGTCAGGAGTTTCTTCGACAAGAAGACCAGCTTCAGGACTATAGGAAGAAAAATACTTACCTTGTGAAGAGGTT
AGAATATCAAAGTTTTCAGTGTGGACAGCAGATCAAGGAATTGAGAGCACAGCATGAAGAAAACATTAAAAAGTTAGTAG
ACCAGTTTTTACAGGAACAAAAGGAAGAGACCCTCAAGATTCAATCAAATGATGGAAAAGAACTGGGTATAAACGATCAA
GTAGTACCTAAAAACATTCCAAAAGTAGCTGAGAATGTTGCAGATAAGAATGAAGAACCCTCAAGCAATCATATTCTACA
TGGGAAAGAACAAATCAAAAGAGGTGGTGATGCAGGGATGCCTGGAATAAAAAAGAATGACCTAGCAAAAGTCGATGATC
TTCCCCCTGCTTTAAGGAAGCCTCCTATTTCAGTTTTTCAACGTGAAAGTCATCAAGCAATCTCCCATCTTCCAACTGGA
CAACCTCTCTCCCCAAATATGCCTCCAGATTCACAGGTAAACCACAATGGAAACCCTGGTACTTCAAAACAGAAGCCTTC
CAGTCCTCTTCAGCGTTTAATTCCAGGCTCAAACTTGGACAGTGAACCAAGAATTCAAACAGATATACTAAAGCAGGCTA
CCAAGGATAGAATCAGTGAGTTCCATAAATTGAAGTAAGGCCACTTCTTTGATGAGAATGAATCTCCTCTTCATCTGCAG
CATGGCTCTAAACTGGCGGATTATAATGGGGATGATGGTAACGTAGGTGAGTATGAGGCAGACAAGCAGGCTGAGCTAGC
TTACAATGGGGAAGAAGATGGTGATGGTGGAGCGGAAGACGTCCAAGATGATGAAGAACGAGAGCTTCAAATGGATCCTG
CAGACTATGGAAAGCAACATTTCAATGATGTCCTT

Alignment

ORF - retro_ptro_852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.8 %
• Parental protein coverage: 69.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELRQEFLRQEDQLQDYRKNNTYLVKRLEYESFQCGQQIKELRAQHEENIKKLADQFLQEQKQETHKIQSN
          ELRQEFLRQEDQLQDYRK.NTYLVKRLEY.SFQCGQQIKELRAQHEENIKKL.DQFLQEQK.ET.KIQSN
Retrocopy ELRQEFLRQEDQLQDYRKKNTYLVKRLEYQSFQCGQQIKELRAQHEENIKKLVDQFLQEQKEETLKIQSN

Parental  DGKELDINNQVVPKNIPKVAENVADKNEEPPSNHIPHGKEQIKRGGDAGMPGIEENDLAKVDDLPPALRK
          DGKEL.IN.QVVPKNIPKVAENVADKNEEP.SNHI.HGKEQIKRGGDAGMPGI..NDLAKVDDLPPALRK
Retrocopy DGKELGINDQVVPKNIPKVAENVADKNEEPSSNHILHGKEQIKRGGDAGMPGIKKNDLAKVDDLPPALRK

Parental  PPISVSQHESHQAISHLPTGQPLSPNMPPDSHVNHNGNPGTSKQNPSSPLQRLIPGSNLDSEPRIQTDIL
          PPISV.Q.ESHQAISHLPTGQPLSPNMPPDS.VNHNGNPGTSKQ.PSSPLQRLIPGSNLDSEPRIQTDIL
Retrocopy PPISVFQRESHQAISHLPTGQPLSPNMPPDSQVNHNGNPGTSKQKPSSPLQRLIPGSNLDSEPRIQTDIL

Parental  KQATKDRVSDFHKLKQSRFFDENESPVDPQHGSKLADYNGDDGNVGEYEADKQAELAYNEEEDGDGGEED
          KQATKDR.S.FHKLK...FFDENESP...QHGSKLADYNGDDGNVGEYEADKQAELAYN.EEDGDGG.ED
Retrocopy KQATKDRISEFHKLK*GHFFDENESPLHLQHGSKLADYNGDDGNVGEYEADKQAELAYNGEEDGDGGAED

Parental  VQDDEERELQMDPADYGKQHFNDVL
          VQDDEERELQMDPADYGKQHFNDVL
Retrocopy VQDDEERELQMDPADYGKQHFNDVL

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	0.05 RPM	51.41 RPM
SRP007412_cerebellum	0.00 RPM	61.87 RPM
SRP007412_heart	0.06 RPM	24.95 RPM
SRP007412_kidney	0.03 RPM	74.74 RPM
SRP007412_liver	0.03 RPM	28.71 RPM
SRP007412_testis	1.90 RPM	62.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_852 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_852 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1238

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006998	4 retrocopies	retro_chof_1422, retro_chof_1445, retro_chof_2453, retro_chof_627,
Homo sapiens	ENSG00000166734	1 retrocopy	retro_hsap_1238,
Nomascus leucogenys	ENSNLEG00000005533	1 retrocopy	retro_nleu_2857,
Oryctolagus cuniculus	ENSOCUG00000005362	1 retrocopy	retro_ocun_1472,
Pongo abelii	ENSPPYG00000006428	1 retrocopy	retro_pabe_1083,
Pan troglodytes	ENSPTRG00000007010	1 retrocopy	retro_ptro_852 ,