RetrogeneDB ID: retro_ggor_2333

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:37696420..37697368(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000025194
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LAP3
• Ensembl ID: ENSGGOG00000001110
• Aliases: None
• Description: None

Sequence

>retro_ggor_2333
ATGATGGAGACGCCAGCCAGCGAGATGATGCCAACCAGATTTGCCGAAATTATTGAGAAGAATCTCAAAAGTGCTAGTAG
TAAACCGAGGTTCATATCAGACCCAGGTCTTGGATTGAGGAACAGGCAATGGGATCATTCCTCAGTGTGGCCAAAGGATC
TGACGAGCCCTCAGTCTTCTTGGAAATTCACTACATAGGCAGCCCCAATGCAGACAAACCACCCCTTGTTTGTTGGGAAA
GGAATTACCTTTGACAGTGGTGGTATCTCCATCAAGGCTTCTGCAAATATGGACCTCATGAGGGCCGACATGGGAGGAGC
TACAACTATATGCTCAGCCATTGTGTCTGCTGCAAAGCTCAATTTGCCCATTAATATTATAGGTCTGGCCCCTCTTTGTG
AAAATATGCCCAGCGGCAAGGCCAACAAGCTGGGGGATGTTGTTAGAGCCAGGAACGGGAAGACCATCCAGGATAACACT
GATGCCGAGGGGAGGCTCATACTGGCTGATGCGCTCTGTTACGTGCACACATTTAACCCGAAGGTCATCCTCAATGCCAC
TACCTTAACAGGTGTCATAGATGTAGCTTTGGGGTCAGGTGCCACTGGGGTCTTTACCAATTCATCCTGGCTCTGGAACA
AGCTCTTCGAGGCCAGCATTGAAACAGGTGACCGTGTCTGGAGGATGCCTCTCTTCAAACATTATACAAGACAGGTTGTA
GATTGCCAGCTGGCTGATGTTAACAACATTGGAAAATATAGATCTGCGGGAGCATGTACATCTGTGGCATTCCTGAAAGA
ATTCGTGACTCATCCTAAGTGGGCACATTTAGACATAGCAGGTGTGATGACCAACAAAGATGAGGTTCCCTATCTATGGA
AAGGCATGACCGGGAGGCCCACAAGGACTCTCATAGAGTTCTTACTTTGTTTCAGTCAAGACAATGCT

Alignment

ORF - retro_ggor_2333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• 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.PTRFAEIIEKNLKSASSK.TEVHIRP.SWIEEQAMGSFLSVAKGSDEP.VFLEIHY.GSP
Retrocopy MMETPASEMMPTRFAEIIEKNLKSASSK<TEVHIRPRSWIEEQAMGSFLSVAKGSDEPSVFLEIHYIGSP

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

Parental  SGKANKPGDVVRAKNGKTIQVDNTDAEGRLILADALCYAHTFNPKVILNAATLTGAMDVALGSGATGVFT
          SGKANK.GDVVRA.NGKTIQ.DNTDAEGRLILADALCY.HTFNPKVILNA.TLTG..DVALGSGATGVFT
Retrocopy SGKANKLGDVVRARNGKTIQ-DNTDAEGRLILADALCYVHTFNPKVILNATTLTGVIDVALGSGATGVFT

Parental  NSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVVDCQLADVNNIGKYRSAGACTAAAFLKEFVTHPKWAH
          NSSWLWNKLFEASIETGDRVWRMPLF.HYTRQVVDCQLADVNNIGKYRSAGACT..AFLKEFVTHPKWAH
Retrocopy NSSWLWNKLFEASIETGDRVWRMPLFKHYTRQVVDCQLADVNNIGKYRSAGACTSVAFLKEFVTHPKWAH

Parental  LDIAGVMTNKDEVPYLRKGMTGRPTRTLIEFLLRFSQDNA
          LDIAGVMTNKDEVPYL.KGMTGRPTRTLIEFLL.FSQDNA
Retrocopy LDIAGVMTNKDEVPYLWKGMTGRPTRTLIEFLLCFSQDNA

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	0.05 RPM	48.63 RPM
SRP007412_cerebellum	0.00 RPM	31.68 RPM
SRP007412_heart	0.00 RPM	40.40 RPM
SRP007412_kidney	0.04 RPM	132.77 RPM
SRP007412_liver	0.05 RPM	129.23 RPM
SRP007412_testis	0.00 RPM	97.69 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2333 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3457
Pan troglodytes	retro_ptro_2344

---

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,