RetrogeneDB ID: retro_ptro_986

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:88601103..88601780(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPPE1
• Ensembl ID: ENSPTRG00000009872
• Aliases: None
• Description: None

Sequence

>retro_ptro_986
ATGGCTATGAGTGGATTGAGGTTTGGAAGACAGAGTTTTCATCCGTTGAAGAGGAAGAGTTGATTGCTGTTGAAATTCAT
TGTCTTTTCTGTGCTTCTGTTTTGTGAATTTTTAATCTATTACTTAGTGATCTTTTGGTGTAATTGGCCTGAAGTGAAAA
CCGCAGCCTATGATGGTGAGCAGGCCACGTGTGAGCCTGTGCTCAAAGCTATGTTTTCGGCTGACACCCACTTGCTTAGG
GAATTCCTAGGTCACTGGCTGGACAAATTACGAAGGGAATGGCAGGTGGAGAGAGCCTTCCAGACAGCTCTGTGGTTGCT
GCAGCCGGAAGTCGTCTTCATCCTGGAGGATGTCTTTGATGAAGGGAAGTGGAGCACCCCTGAGGCCTGGGTGGATGATG
TGGAGCAGTTTCGGAAAATGTTCAGACACCCAAGTCATGTGCAGCTGAAGGTAGTTGCTGGAAACCATGACATTGGCTTC
CACTATGAGATGAACACATACGAAGTAGAACGGTTTGAGAAAGTGTTCATCTCTGAAAGCCTGTTTTCTTGGAAAGGATT
AACTTCATGATGGTCAACAGCATGGCACTGAAGGGGGACAGCTGTGGCATCTGTTCTGAAGCAGAAGCAGAAGCAGAGCT
CACTGAAGTTTCTTACAGACTGAATTGCTCCCAAGAG

Alignment

ORF - retro_ptro_986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.53 %
• Parental protein coverage: 57.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMIELGFGRQNFHPLKRKSSLLLKLIAVVFAVLLFCEFLIYYLAIFQCNWPEVKTTASDGEQATREPVL
          MAM..L.FGRQ.FHPLKRKS.LLLK.I..VF.VLLFCEFLIYYL.IF.CNWPEVKT.A.DGEQAT.EPVL
Retrocopy MAMSGLRFGRQSFHPLKRKS*LLLKFI--VFSVLLFCEFLIYYLVIFWCNWPEVKTAAYDGEQATCEPVL

Parental  KAMFLADTHLLGEFLGHWLDKLRREWQMERAFQTALWLLQPEVVFILGDIFDEGKWSTPEAWADDVERFQ
          KAMF.ADTHLL.EFLGHWLDKLRREWQ.ERAFQTALWLLQPEVVFIL.D.FDEGKWSTPEAW.DDVE.F.
Retrocopy KAMFSADTHLLREFLGHWLDKLRREWQVERAFQTALWLLQPEVVFILEDVFDEGKWSTPEAWVDDVEQFR

Parental  KMFRHPSHVQLKVVAGNHDIGFHYEMNTYKVERFEKVFSSERLFSWKG-INFVMVNSVALNGDGCGICS-
          KMFRHPSHVQLKVVAGNHDIGFHYEMNTY.VERFEKVF.SE.LFSWKG.INF.MVNS.AL.GD.CGICS.
Retrocopy KMFRHPSHVQLKVVAGNHDIGFHYEMNTYEVERFEKVFISESLFSWKG<INFMMVNSMALKGDSCGICSX

Parental  -ETEAELIEVSHRLNCSRE
          ......L.EVS.RLNCS.E
Retrocopy XXXXXXLTEVSYRLNCSQE

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	30.12 RPM
SRP007412_cerebellum	0.00 RPM	25.95 RPM
SRP007412_heart	0.00 RPM	16.88 RPM
SRP007412_kidney	0.00 RPM	66.77 RPM
SRP007412_liver	0.03 RPM	58.89 RPM
SRP007412_testis	0.11 RPM	20.23 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_986 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_986 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1450
Pongo abelii	retro_pabe_3557

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154889	1 retrocopy	retro_hsap_1450,
Macaca mulatta	ENSMMUG00000011467	1 retrocopy	retro_mmul_2270,
Mus musculus	ENSMUSG00000062526	1 retrocopy	retro_mmus_869,
Otolemur garnettii	ENSOGAG00000007068	2 retrocopies	retro_ogar_1163, retro_ogar_2826,
Pongo abelii	ENSPPYG00000008997	1 retrocopy	retro_pabe_3557,
Pan troglodytes	ENSPTRG00000009872	1 retrocopy	retro_ptro_986 ,