RetrogeneDB ID: retro_ptro_2630

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:62989017..62989823(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPZL1
• Ensembl ID: ENSPTRG00000024131
• Aliases: None
• Description: None

Sequence

>retro_ptro_2630
ATGGCAGCACCCGCTGGAGCCGGGGCAGTGATTGCAGCCCCAGACAGGAGGCGCTGGCTGTGGTCGGTGCTGGCAGTGGC
GCTGGGGCTCTTGACAGCTGGAGTATCAGCCTTGGAAGTATATTTACCAAAAGAAATCTTCGTGGCAAATGGTACACAAG
GGAAGCTGACCTGCAAGTTCAAGTCTACTAATACGACTGGCGGGTTGACCTCAGTCTCCTGGAGCTTCCAGCCGAGGGGG
CCGACACCACCGTGTCATTTTACCACTACTCCCAAGGGCAAGTGTACTTCGGGAATTATCCACCATTTAAAGACAGAATC
AGCTGGGCTGGAGACCTTGACAAGAAAGATGCAACAATCAACATAGAAAATATGCAGTTTATACACAATGGCACCTATAT
CTGTGATGCCAAAAACCCTCCTGACATTGTTGTCCAGCCTGGACACATTAGACTCTATGTCGTAGAAAAAGAGAGTTTGC
CTGTGTTTCCAGTTTGGGTAGTGGTGGGCATAGTTACTGCTGTGGTCCTAGGTCTCACTCTGCTCATCAGCCTGATTCTG
GCTGTCTTCTATAGAAGGTGAAACTCTAAATGGGATTACACTGGCTGCAGTACATCAGAGAGTTTATCACCAGTTAAGCA
GGCTCGTCGGAAGTCCCCTTCTGACACTGAGGGTCTTGTAAAGAGTCTGCCTTCTGGATCTCACCAGGGCCCAGTCATAT
ATGCACAGTTAGACCACTCTAGCGGACATCAGAGTGACAAGATTAACAAGTCAGAGTCTGTGGTGTATGTGGATATCCAG
AAAAAT

Alignment

ORF - retro_ptro_2630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPAGAGAVIAAPDSRRWLWSVLAAALGLLTAGVSALEVYTPKEIFVANGTQGKLTCKFKSTSTTGGLT
          MAAPAGAGAVIAAPD.RRWLWSVLA.ALGLLTAGVSALEVY.PKEIFVANGTQGKLTCKFKST.TTGGLT
Retrocopy MAAPAGAGAVIAAPDRRRWLWSVLAVALGLLTAGVSALEVYLPKEIFVANGTQGKLTCKFKSTNTTGGLT

Parental  SVSWSFQP-EGADTTVSFFHYSQGQVYLGNYPPFKDRISWAGDLDKKDASINIENMQFIHNGTYICDVKN
          SVSWSFQP.EGADTTVSF.HYSQGQVY.GNYPPFKDRISWAGDLDKKDA.INIENMQFIHNGTYICD.KN
Retrocopy SVSWSFQP<EGADTTVSFYHYSQGQVYFGNYPPFKDRISWAGDLDKKDATINIENMQFIHNGTYICDAKN

Parental  PPDIVVQPGHIRLYVVEKENLPVFPVWVVVGIVTAVVLGLTLLISMILAVLYRRKNSKRDYTGCSTSESL
          PPDIVVQPGHIRLYVVEKE.LPVFPVWVVVGIVTAVVLGLTLLIS.ILAV.YRR.NSK.DYTGCSTSESL
Retrocopy PPDIVVQPGHIRLYVVEKESLPVFPVWVVVGIVTAVVLGLTLLISLILAVFYRR*NSKWDYTGCSTSESL

Parental  SPVKQAPRKSPSDTEGLVKSLPSGSHQGPVIYAQLDHSGGHHSDKINKSESVVYADIRKN
          SPVKQA.RKSPSDTEGLVKSLPSGSHQGPVIYAQLDHS.GH.SDKINKSESVVY.DI.KN
Retrocopy SPVKQARRKSPSDTEGLVKSLPSGSHQGPVIYAQLDHSSGHQSDKINKSESVVYVDIQKN

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	30.80 RPM
SRP007412_cerebellum	0.00 RPM	31.33 RPM
SRP007412_heart	0.00 RPM	26.29 RPM
SRP007412_kidney	0.03 RPM	58.27 RPM
SRP007412_liver	0.00 RPM	26.22 RPM
SRP007412_testis	0.11 RPM	56.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2630 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2630 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3048

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000197965	1 retrocopy	retro_hsap_3859,
Macaca mulatta	ENSMMUG00000009184	1 retrocopy	retro_mmul_1608,
Pongo abelii	ENSPPYG00000000548	1 retrocopy	retro_pabe_3048,
Pan troglodytes	ENSPTRG00000024131	1 retrocopy	retro_ptro_2630 ,