RetrogeneDB ID: retro_ptro_3061

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392675.1:76755..77457(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEIS3
• Ensembl ID: ENSPTRG00000011208
• Aliases: MEIS3, MEIS3P1
• Description: Meis homeobox 3 [Source:UniProtKB/TrEMBL;Acc:K7AKH6]

Sequence

>retro_ptro_3061
TACGATGAGCTGCCGCACTACCCAGGCATCACGGATGGCCCCGCAGCCCTGGCTGGCTTCCCAGAGGCAGTGCCCGCGGC
ACCAGGGCCCTATGGCCCTCACCGGCCTCCCCAGCCCCTACCCCCAGGCTTGGACAGCGACGGCCTCAAGAGGGACAAGG
ATGAGATCTGTGGACACCCGCTCTTCCCCCTCTTGGCCCTGGTCTTTGAGAAATGTGAACTGGCTACATGCTCTCCCCGT
GATGGGGCCGGAGCTGGGCTGGGGACACCCTGCGGCGGTGACGTCTGCTCCTCTGATTCCTTCAACGAGGACAACACTGC
CTTTGCCAAGCAGGTTCGCTCTTAGAGGCCCTTCTCCTCCAACCCAGAACTGGACAATCTGATGATCCAGGCCATCCAAG
TGCTGCGGTTCCACCTGCTGGAGCTGGAGAAGGGAAAGATGCCCATCGACCTGGTCATCGAGGATCGGGATGGCGGCTGC
AGGGAGGACTTCGAGGACTACCCAGCCTCCTGCCCCAGCCTCCCAGACCAGAATAATATATGGATTCGAGACCATGAGGA
TAGCGGGTCTGTACATTTGGGGACCCCAGGTCCATCCAGCGGGGGCCTGGCCTCCCAGAGTGGGGACAACTCCAGTGACC
AAGGAGTCGGGCTGGACACCAGCGTGGCCTCTCCCAGTTCTGGTGGAGAAGATGAGGACTTG

Alignment

ORF - retro_ptro_3061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.07 %
• Parental protein coverage: 58.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YDELPHYPGIVDGPAALAGFPEAVTAVPGPYGPHRPPQPLPPGLDSDGLKREKDEIYGHPLFPLLALVFE
          YDELPHYPGI.DGPAALAGFPEAV.A.PGPYGPHRPPQPLPPGLDSDGLKR.KDEI.GHPLFPLLALVFE
Retrocopy YDELPHYPGITDGPAALAGFPEAVPAAPGPYGPHRPPQPLPPGLDSDGLKRDKDEICGHPLFPLLALVFE

Parental  KCELATCSPRDGAGAGLGTPHGGDVCSSDSFNEDIAAFAKQVRSERPLFSSNPELDNLMIQAIQVLRFHL
          KCELATCSPRDGAGAGLGTP.GGDVCSSDSFNED..AFAKQVRS.RP.FSSNPELDNLMIQAIQVLRFHL
Retrocopy KCELATCSPRDGAGAGLGTPCGGDVCSSDSFNEDNTAFAKQVRS*RP-FSSNPELDNLMIQAIQVLRFHL

Parental  LELEKKGKMPIDLVIEDRDGGYREDFEDYPASCPSLPDQNNMWIRDHEDSGSVHLGTPGPSSGGLASQSG
          LELE.KGKMPIDLVIEDRDGG.REDFEDYPASCPSLPDQNN.WIRDHEDSGSVHLGTPGPSSGGLASQSG
Retrocopy LELE-KGKMPIDLVIEDRDGGCREDFEDYPASCPSLPDQNNIWIRDHEDSGSVHLGTPGPSSGGLASQSG

Parental  DNSSDQGDGLDTSVASPSSGGEDEDL
          DNSSDQG.GLDTSVASPSSGGEDEDL
Retrocopy DNSSDQGVGLDTSVASPSSGGEDEDL

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	0.30 RPM	46.44 RPM
SRP007412_cerebellum	0.25 RPM	13.77 RPM
SRP007412_heart	0.00 RPM	0.70 RPM
SRP007412_kidney	0.03 RPM	1.52 RPM
SRP007412_liver	0.00 RPM	0.92 RPM
SRP007412_testis	0.42 RPM	23.82 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3061 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3061 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105419	2 retrocopies	retro_hsap_1718, retro_hsap_1731,
Gorilla gorilla	ENSGGOG00000001093	1 retrocopy	retro_ggor_2263,
Mustela putorius furo	ENSMPUG00000004760	1 retrocopy	retro_mputfur_69,
Pan troglodytes	ENSPTRG00000011208	1 retrocopy	retro_ptro_3061 ,