RetrogeneDB ID: retro_ptro_2344

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:37150715..37151666(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAP3
• Ensembl ID: ENSPTRG00000015938
• Aliases: None
• Description: Pan troglodytes leucine aminopeptidase 3 (LAP3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246465]

Sequence

>retro_ptro_2344
ATGATGGAGACGCCAGCCAGCGAGATGATGCCAACCAGATTTGCCGAAATTATTGAGAAGAATCTCAAAAGTGCTTGTAG
TAAACCGAGGTTCATATCAGACCCAGGTCTTGGATTGAGGAACAGGCAATGGGATCATTCCTCAGTGTGGCCAAAGGATC
TGACGAGCCCTCAGTCTTCTTGGAAATTCACTACATAGGCAGCCCCAATGCAGACAAACCACCCCTTGTTTGTTGGGAAA
GGAATTACCTTTGACAGTGGTGGTATCTCCATCAAGGCTTCTGCAAATATGGACCTCATGAGGGCCGACATGGGAGGAGC
TACAACTATATGCTCAGCCATTGTGTCTGCTGCAAAGCTCAATTTGCCCATTAATATTATAGGTCTGGCCCCCCTTTGTG
AAAATATGCCCAGCGGCAAGGCCAACAAGCTGGGGGATGTTGGTAGAGCCAGGAACGGGAAGACCATCCAGGTTGATAAC
ACTGATGCCGAGGGGAGGCTCATACTGGCTGATGCGCTCTGTTACGTGCACACATTTAACCTGAAGGTCATCCTCAATGC
CACCACCTTAACAGGTGTCATAGATGTAGCTTTGGGGTCAGGTTCCACTGGGGTCTTTACCAATTCATCCTGGCTCTGGA
ACAAGCTCTTGCAGGCCAGCATTGAAACAGGGGACCGTGTCTGGAGGATGCCTCTCTTCAAACATTATACAAGACAGGTT
GTAGGTTGCCAGCTGGCTGATGTTAACAACATTGGAAAATATAGATCTGCGGGAGCATGTACATCTGTGGCATTCCTGAA
AGAATTTGTGACTCATCCTAAGTGGGCACATTTAGGCATAGCAGTTGTGATGACCAACAAAAATAAGGTTCCCTATCTAT
GGAAAGGCATGACCGGGAGGCCCACAAGGACTCTCATAGAGTTCTTACTTCGTTTCAGTCAAGACAATGCT

Alignment

ORF - retro_ptro_2344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.69 %
• Parental protein coverage: 61.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LMETPANEMTPTRFAEIIEKNLKSASSK-TEVHIRPKSWIEEQAMGSFLSVAKGSDEPPVFLEIHYKGSP
          .METPA.EM.PTRFAEIIEKNLKSA.SK.TEVHIRP.SWIEEQAMGSFLSVAKGSDEP.VFLEIHY.GSP
Retrocopy MMETPASEMMPTRFAEIIEKNLKSACSK<TEVHIRPRSWIEEQAMGSFLSVAKGSDEPSVFLEIHYIGSP

Parental  NANEP-PLVFVGKGITFDSGGISIKASANMDLMRADMGGAATICSAIVSAAKLNLPINIIGLAPLCENMP
          NA..P.PL.FVGKGITFDSGGISIKASANMDLMRADMGGA.TICSAIVSAAKLNLPINIIGLAPLCENMP
Retrocopy NADKP>PL-FVGKGITFDSGGISIKASANMDLMRADMGGATTICSAIVSAAKLNLPINIIGLAPLCENMP

Parental  SGKANKPGDVVRAKNGKTIQVDNTDAEGRLILADALCYAHTFNPKVILNAATLTGAMDVALGSGATGVFT
          SGKANK.GDV.RA.NGKTIQVDNTDAEGRLILADALCY.HTFN.KVILNA.TLTG..DVALGSG.TGVFT
Retrocopy SGKANKLGDVGRARNGKTIQVDNTDAEGRLILADALCYVHTFNLKVILNATTLTGVIDVALGSGSTGVFT

Parental  NSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVVDCQLADVNNIGKYRSAGACTAAAFLKEFVTHPKWAH
          NSSWLWNKL..ASIETGDRVWRMPLF.HYTRQVV.CQLADVNNIGKYRSAGACT..AFLKEFVTHPKWAH
Retrocopy NSSWLWNKLLQASIETGDRVWRMPLFKHYTRQVVGCQLADVNNIGKYRSAGACTSVAFLKEFVTHPKWAH

Parental  LDIAGVMTNKDEVPYLRKGMTGRPTRTLIEFLLRFSQDNA
          L.IA.VMTNK..VPYL.KGMTGRPTRTLIEFLLRFSQDNA
Retrocopy LGIAVVMTNKNKVPYLWKGMTGRPTRTLIEFLLRFSQDNA

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	29.56 RPM
SRP007412_cerebellum	0.00 RPM	79.76 RPM
SRP007412_heart	0.09 RPM	146.34 RPM
SRP007412_kidney	0.05 RPM	321.98 RPM
SRP007412_liver	0.23 RPM	926.25 RPM
SRP007412_testis	0.11 RPM	139.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2344 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2344 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3457
Gorilla gorilla	retro_ggor_2333

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004383	1 retrocopy	retro_cint_4,
Homo sapiens	ENSG00000002549	1 retrocopy	retro_hsap_3457,
Gorilla gorilla	ENSGGOG00000001110	1 retrocopy	retro_ggor_2333,
Nomascus leucogenys	ENSNLEG00000016606	1 retrocopy	retro_nleu_2711,
Pongo abelii	ENSPPYG00000014626	1 retrocopy	retro_pabe_2858,
Pan troglodytes	ENSPTRG00000015938	1 retrocopy	retro_ptro_2344 ,
Rattus norvegicus	ENSRNOG00000003289	1 retrocopy	retro_rnor_1332,
Tursiops truncatus	ENSTTRG00000006175	1 retrocopy	retro_ttru_1013,