RetrogeneDB ID: retro_pabe_2858

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:36711010..36711964(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAP3
• Ensembl ID: ENSPPYG00000014626
• Aliases: None
• Description: leucine aminopeptidase 3 [Source:HGNC Symbol;Acc:18449]

Sequence

>retro_pabe_2858
ATGATGGAGATGCCAGCCAGCGAGATGATGCCAACCAGATTTGCCGAAATTATTGAGAAGAATCTCAAAAGTGCTAGTAG
TAAAACTGAGGTTCATATCAGACCCAGGTCTTGGATTGAGGAACAGGCAATGGGATCATTCCTCAGTGTGGCCAAAGGAT
CTGATGGGCCCCCAGTCTTCTTGGAAATTCACTACATAGGCAGCCCCAATGCAAACGAACCACCCCTGGTGTTTGTTGGG
AAAGGAATTACCTTTGACAGTGGTGGTATCTCCATCAAGGCTTCTGCAAATATGGAACTCATGAGGGCCGACATGGGAGG
AGCTACAATTATATGCTCAGCCATCGTGTCTGCTGCAAAGCTCAATTTGCCCATTAATATTATAGGTCTGGCCCCTCTTT
GTGAAAATATGCCCAGCGGCAAGGCCAACAAGCTGGGGGATGTTGTTTGAGCCAGGAACGGGAAGACCATTCAGGTTGAT
AACACTGATGCCGAGGGGAGGCTCATACTGGCTGATGCGCTCTGTTACGCGCACACGTTTAACCCGAAGGTCATCCTCAA
TGCCACCACCTTAACAGGTGTCATAGATGTAGCTTTGGGGTCAGGTGCCACTGGGGTCTTTACCAATTCATCCTGGCTCT
GGAACAAGCTCTTCGAGGCCAGCATTGAAATAGGGGACCCTGTCTGGAGGATGCCTCTCTTCAAACATTATACAAGACAG
GTTGTAGATTGCCAGCTGGCTGATGTTAACAACATTGGAAAATATAGATCTGCGGGAGCATGTACATCTGCGGCATTCCT
GAAAGAATTCGTGACTCATCCTAAGTGGGCACATTTATACATAGCAGGTGTGATGACCAACAAAGATGAAGTTCCCTATC
TACGGAAGGGCATGACCGGGAGGCCCACAAGGACTCTCACAGAGTTCTTACTTCATTTCAGTCAAGACAATGCT

Alignment

ORF - retro_pabe_2858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.77 %
• Parental protein coverage: 61.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LMETPANEMTPTRFAEIIEKNLKSASSKTEVHIRPKSWIEEQAMGSFLSVAKGSDEPPVFLEIHYKGSPN
          .ME.PA.EM.PTRFAEIIEKNLKSASSKTEVHIRP.SWIEEQAMGSFLSVAKGSD.PPVFLEIHY.GSPN
Retrocopy MMEMPASEMMPTRFAEIIEKNLKSASSKTEVHIRPRSWIEEQAMGSFLSVAKGSDGPPVFLEIHYIGSPN

Parental  ANEPPLVFVGKGITFDSGGISIKASANMDLMRADMGGAATICSAIVSAAKLNLPINIIGLAPLCENMPSG
          ANEPPLVFVGKGITFDSGGISIKASANM.LMRADMGGA..ICSAIVSAAKLNLPINIIGLAPLCENMPSG
Retrocopy ANEPPLVFVGKGITFDSGGISIKASANMELMRADMGGATIICSAIVSAAKLNLPINIIGLAPLCENMPSG

Parental  KANKPGDVVRAKNGKTIQVDNTDAEGRLILADALCYAHTFNPKVILNAATLTGAMDVALGSGATGVFTNS
          KANK.GDVV.A.NGKTIQVDNTDAEGRLILADALCYAHTFNPKVILNA.TLTG..DVALGSGATGVFTNS
Retrocopy KANKLGDVV*ARNGKTIQVDNTDAEGRLILADALCYAHTFNPKVILNATTLTGVIDVALGSGATGVFTNS

Parental  SWLWNKLFEASIETGDRVWRMPLFEHYTRQVVDCQLADVNNIGKYRSAGACTAAAFLKEFVTHPKWAHLD
          SWLWNKLFEASIE.GD.VWRMPLF.HYTRQVVDCQLADVNNIGKYRSAGACT.AAFLKEFVTHPKWAHL.
Retrocopy SWLWNKLFEASIEIGDPVWRMPLFKHYTRQVVDCQLADVNNIGKYRSAGACTSAAFLKEFVTHPKWAHLY

Parental  IAGVMTNKDEVPYLRKGMTGRPTRTLIEFLLRFSQDNA
          IAGVMTNKDEVPYLRKGMTGRPTRTL.EFLL.FSQDNA
Retrocopy IAGVMTNKDEVPYLRKGMTGRPTRTLTEFLLHFSQDNA

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	33.62 RPM
SRP007412_cerebellum	0.00 RPM	25.29 RPM
SRP007412_heart	0.03 RPM	43.44 RPM
SRP007412_kidney	0.07 RPM	105.77 RPM
SRP007412_liver	0.15 RPM	163.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2858 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2858 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2858 has 0 orthologous retrocopies within eutheria group .

---

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,