RetrogeneDB ID: retro_ggor_2084

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:180378352..180378838(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000026687
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLNS1A
• Ensembl ID: ENSGGOG00000003091
• Aliases: None
• Description: None

Sequence

>retro_ggor_2084
TATTTGTATGTTATGGTGAAAGCCAAATTTGAAGAAGGATCAAAAGAATCTGTTGCTGACGAAGAAGAGGAAAATAGTGA
TAATGATAATGATGTGGAACTATTACTGAATTTAGATTTGTGCCTAGTGATAAATCAACATTGGAGGCAATGTTCACTGC
AATGTGTGAATGCCAGTACTTGCATCCAGATGCTGAGGATGAAGATTCAGATGCTTACGATGGAGAAGAATATGATGTGG
AAGCGCAAGAACAAGGACATGGGGACATCCCTACATTTTACACCTGTGAGGAAGGATTTATCTCATCTAACAGCAGAGGG
CCAAACATGTTGGAGATTAGAAGGAACGCTTTCTCAGTCTGTAAGCTGCCAGTATCATATGGTTGGGGTCAGGACAGAAG
ACTCAATAAGAGATGATGAAGCTGGGATGGAGGTGGATACCACACCAACAGTTGCTGGACAGTTTGAGGATGCAGATGTT
GATCAC

Alignment

ORF - retro_ggor_2084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.64 %
• Parental protein coverage: 66.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HLYVMVNAKFEEESKEPVADEEEE--DSDDDVE-PITEFRFVPSDKSALEAMFTAMCECQALHPDPEDED
          .LYVMV.AKFEE.SKE.VADEEEE..D.D.DVE..ITEFRFVPSDKS.LEAMFTAMCECQ.LHPD.EDED
Retrocopy YLYVMVKAKFEEGSKESVADEEEENSDNDNDVE<TITEFRFVPSDKSTLEAMFTAMCECQYLHPDAEDED

Parental  SDDYDGEEYDVEAHEQGQGDIPTFYTYEEG-LSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTEDSIR
          SD.YDGEEYDVEA.EQG.GDIPTFYT.EEG.LSHLTAEGQ.T..RLEG.LSQSVS.QY.M.GVRTEDSIR
Retrocopy SDAYDGEEYDVEAQEQGHGDIPTFYTCEEG>LSHLTAEGQ-TCWRLEGTLSQSVSCQYHMVGVRTEDSIR

Parental  DYEDGMEVDTTPTVAGQFEDADVDH
          D.E.GMEVDTTPTVAGQFEDADVDH
Retrocopy DDEAGMEVDTTPTVAGQFEDADVDH

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	36.92 RPM
SRP007412_cerebellum	0.00 RPM	36.84 RPM
SRP007412_heart	0.09 RPM	10.16 RPM
SRP007412_kidney	0.00 RPM	38.89 RPM
SRP007412_liver	0.08 RPM	34.45 RPM
SRP007412_testis	0.31 RPM	45.27 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_2084 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2084 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3010
Pongo abelii	retro_pabe_2494

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019930	1 retrocopy	retro_btau_376,
Canis familiaris	ENSCAFG00000004900	6 retrocopies	retro_cfam_1112, retro_cfam_1448, retro_cfam_255, retro_cfam_327, retro_cfam_720, retro_cfam_727,
Callithrix jacchus	ENSCJAG00000014927	1 retrocopy	retro_cjac_4085,
Cavia porcellus	ENSCPOG00000005260	1 retrocopy	retro_cpor_67,
Felis catus	ENSFCAG00000026321	1 retrocopy	retro_fcat_736,
Homo sapiens	ENSG00000074201	2 retrocopies	retro_hsap_3010, retro_hsap_3595,
Gorilla gorilla	ENSGGOG00000003091	1 retrocopy	retro_ggor_2084 ,
Macropus eugenii	ENSMEUG00000005935	4 retrocopies	retro_meug_1825, retro_meug_2097, retro_meug_783, retro_meug_929,
Mus musculus	ENSMUSG00000025439	1 retrocopy	retro_mmus_1984,
Nomascus leucogenys	ENSNLEG00000016699	2 retrocopies	retro_nleu_300, retro_nleu_756,
Oryctolagus cuniculus	ENSOCUG00000024393	1 retrocopy	retro_ocun_1303,
Pongo abelii	ENSPPYG00000003712	1 retrocopy	retro_pabe_2494,
Sorex araneus	ENSSARG00000009460	2 retrocopies	retro_sara_247, retro_sara_682,
Ictidomys tridecemlineatus	ENSSTOG00000027980	3 retrocopies	retro_itri_239, retro_itri_319, retro_itri_490,