RetrogeneDB ID: retro_ggor_1874

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:113219015..113219644(+)
• Located in intron of: ENSGGOG00000009490

Retrocopy information

• Ensembl ID: ENSGGOG00000022549
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CTDNEP1
• Ensembl ID: ENSGGOG00000013777
• Aliases: None
• Description: None

Sequence

>retro_ggor_1874
GTAATTCAGTACCAAACTGTTCGATATGATATCCTCCCCTTATCTCCTGTGTCCCGGAATCGGCTATCCCAGGTGAAGAG
GAAGATCCTGGTGCTGGATCTGGATGAGACACTTATTCACTCCCACCATGATGGGGTCCTGAGGCCGCAGTCCGGCCTGG
TACGCTTCCTGACTTCATCCTCAAGGTGGTAATAGACAAACATCCTGTCCGGTTTTTTGTACGTAAGAGGCCCCATGTGG
ATTTCTTCCTGGAAGTGGTGAGCCAGTGGTACGAGCTGGTCGTGTTTACAGAAAGCATGGAGATCTATGGCTCTGCTGTG
GCAGGTAAACTGGACATTAGCAGAAGCATCCTTAAGAGGAGATATTACAGACAGCACTGCACTTTGGAGTTGAGCAGCTA
CATCAAGGACCTCTCTGTGGTCCACAGTGACCTCTCCAGCATTGTGATCCTGGATAACTCCCCAGGGGCTTACTGGAGCC
ATCCAGACAATGCCATCCCCATCAAATCCTGGTTCAGTGACCCCAGCGACACAGCCCTTCTCAACCTGCTCCCGATGCTG
GATGCCCTCAGGTTCACCGCTGACGTTCGTTCCGTGCTGAGTCGAAACCTTCACCAACATCGGCTCTGG

Alignment

ORF - retro_ggor_1874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VIQYQTVRYDILPLSPVSRNRLAQVKRKILVLDLDETLIHSHHDGVLRP-TVRPGTPPDFILKVVIDKHP
          VIQYQTVRYDILPLSPVSRNRL.QVKRKILVLDLDETLIHSHHDGVLRP..VRPGT.PDFILKVVIDKHP
Retrocopy VIQYQTVRYDILPLSPVSRNRLSQVKRKILVLDLDETLIHSHHDGVLRP<AVRPGTLPDFILKVVIDKHP

Parental  VRFFVHKRPHVDFFLEVVSQWYELVVFTASMEIYGSAVADKLDNSRSILKRRYYRQHCTLELGSYIKDLS
          VRFFV.KRPHVDFFLEVVSQWYELVVFT.SMEIYGSAVA.KLD.SRSILKRRYYRQHCTLEL.SYIKDLS
Retrocopy VRFFVRKRPHVDFFLEVVSQWYELVVFTESMEIYGSAVAGKLDISRSILKRRYYRQHCTLELSSYIKDLS

Parental  VVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFSDPSDTALLNLLPMLDALRFTADVRSVLSRNLHQHRL
          VVHSDLSSIVILDNSPGAY.SHPDNAIPIKSWFSDPSDTALLNLLPMLDALRFTADVRSVLSRNLHQHRL
Retrocopy VVHSDLSSIVILDNSPGAYWSHPDNAIPIKSWFSDPSDTALLNLLPMLDALRFTADVRSVLSRNLHQHRL

Parental  W
          W
Retrocopy W

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	3.12 RPM	40.95 RPM
SRP007412_cerebellum	3.19 RPM	41.05 RPM
SRP007412_heart	1.97 RPM	22.01 RPM
SRP007412_kidney	2.66 RPM	43.71 RPM
SRP007412_liver	1.64 RPM	27.20 RPM
SRP007412_testis	4.25 RPM	42.48 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_1874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1874 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2687
Pan troglodytes	retro_ptro_1814
Pongo abelii	retro_pabe_2294

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019443	1 retrocopy	retro_btau_915,
Dasypus novemcinctus	ENSDNOG00000013673	2 retrocopies	retro_dnov_1802, retro_dnov_2494,
Echinops telfairi	ENSETEG00000004654	1 retrocopy	retro_etel_125,
Homo sapiens	ENSG00000175826	2 retrocopies	retro_hsap_2687, retro_hsap_3188,
Gorilla gorilla	ENSGGOG00000013777	2 retrocopies	retro_ggor_1338, retro_ggor_1874 ,
Macaca mulatta	ENSMMUG00000010547	1 retrocopy	retro_mmul_2011,
Mus musculus	ENSMUSG00000018559	1 retrocopy	retro_mmus_1023,
Otolemur garnettii	ENSOGAG00000004389	1 retrocopy	retro_ogar_1001,
Pongo abelii	ENSPPYG00000007902	2 retrocopies	retro_pabe_2294, retro_pabe_2645,
Pan troglodytes	ENSPTRG00000008668	2 retrocopies	retro_ptro_1814, retro_ptro_2256,
Drosophila melanogaster	FBgn0029067	1 retrocopy	retro_dmel_18,