RetrogeneDB ID: retro_ggor_1372

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:23679877..23680812(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022607
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CIAPIN1
• Ensembl ID: ENSGGOG00000012402
• Aliases: None
• Description: None

Sequence

>retro_ggor_1372
ATGGCAGATTTTGGGATCTCTGCTGGCCAGTTTGTGGCAGTGGCCTGGGATAAGTCATCCCCAGTGGAGGCTCTGAAAGG
TCTGGTGGATGAGCTTCAAGGTTAACTGGCAATGAGGGCCGTGTGTCTGTGGAAAACATCAACCAGCTGTTGCAGTCTGC
CCACAAAGAATCCAGCTTTGACATTATTTTGTCGGGTTTAGTCCCGGGAAGCACCACTCTGCACAGTGCTGAGATTTTGG
CTGAAATCGCCTGGATCCTTCGGCCTGGTGGATGTCTTTTTCTGAAAAAGCCAGTAAAGACAGCTGTAGATAACAATAGC
AAAGTGAAGACAGCATCTAAGCTGTGTTCAGCCCTGATTCTTTCTGGTCTTGTGGAAGTGAAAGAGCTGCAGCGGGAGCC
CCTAACCCCTGAGGAAATACAGTCTGTTCGAGAACACCTTGGTCGTGAAAGTGACAGCCTGCTGTTTGTTCAGATCACAG
GCAAAAAACAAAACTTTGAAGTGGGTTCTTCTAGTCAGCTTAAGATTTCCATCACCAAGAAGTCTTCTCCTTCAGTGAAG
CCTGCTGTGGACCCTGCTGCTGCCAAGCTGTGGACCCTCTCAGCCAACGATATGGAGGACGACAGCATGGATCTCATTGA
CTCAGATGAGCTGCTGGATCCAGAAGATTTGAAGAAGCCAGATCCGGCTTCCCTGCGGGCTGCTTCTTGTGGGGAAGGGA
AAAAGAGGAAGGCCTGTAAGAACTGCACCTGTGGCCTTGCCAAAACACTGGAAAAAGAGAAGTCAAGGGAACAGATGAGC
TCCCAACCCAAGTCGGCTTGTGGAAACTGCTACCTGGGCGATGCCTTCCGCTGTGCCAGCTGCCCCTACCTTGGGATGCC
AGCCTTCAAACCTAGGGAAAAGGTGCTTCTGAGCAACAGCAATCTTCACGATGCC

Alignment

ORF - retro_ggor_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADFGISAGQFVAVVWDKSSPVEALKGLVDKLQA-LTGNEGRVSVENINQLLQSAHKESSFDIILSGLVP
          MADFGISAGQFVAV.WDKSSPVEALKGLVD.LQ..LTGNEGRVSVENINQLLQSAHKESSFDIILSGLVP
Retrocopy MADFGISAGQFVAVAWDKSSPVEALKGLVDELQG<LTGNEGRVSVENINQLLQSAHKESSFDIILSGLVP

Parental  GSTTLHSAEILAEIARILRPGGCLFLKEPVETAVDNNSKVKTASKLCSALTLSGLVEVKELQREPLTPEE
          GSTTLHSAEILAEIA.ILRPGGCLFLK.PV.TAVDNNSKVKTASKLCSAL.LSGLVEVKELQREPLTPEE
Retrocopy GSTTLHSAEILAEIAWILRPGGCLFLKKPVKTAVDNNSKVKTASKLCSALILSGLVEVKELQREPLTPEE

Parental  VQSVREHLGHESDNLLFVQITGKKPNFEVGSSRQLKLSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS
          .QSVREHLG.ESD.LLFVQITGKK.NFEVGSS.QLK.SITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS
Retrocopy IQSVREHLGRESDSLLFVQITGKKQNFEVGSSSQLKISITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS

Parental  MDLIDSDELLDPEDLKKPDPASLRAASCGEGKKRKACKNCTCGLAEELEKEKSREQMSSQPKSACGNCYL
          MDLIDSDELLDPEDLKKPDPASLRAASCGEGKKRKACKNCTCGLA..LEKEKSREQMSSQPKSACGNCYL
Retrocopy MDLIDSDELLDPEDLKKPDPASLRAASCGEGKKRKACKNCTCGLAKTLEKEKSREQMSSQPKSACGNCYL

Parental  GDAFRCASCPYLGMPAFKPGEKVLLSDSNLHDA
          GDAFRCASCPYLGMPAFKP.EKVLLS.SNLHDA
Retrocopy GDAFRCASCPYLGMPAFKPREKVLLSNSNLHDA

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	0.19 RPM	29.54 RPM
SRP007412_cerebellum	0.04 RPM	23.60 RPM
SRP007412_heart	0.03 RPM	14.79 RPM
SRP007412_kidney	0.12 RPM	36.43 RPM
SRP007412_liver	0.03 RPM	20.36 RPM
SRP007412_testis	0.10 RPM	110.96 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_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1372 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1875
Pan troglodytes	retro_ptro_1258
Pongo abelii	retro_pabe_1556

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012055	1 retrocopy	retro_cjac_2575,
Homo sapiens	ENSG00000005194	1 retrocopy	retro_hsap_1875,
Gorilla gorilla	ENSGGOG00000012402	1 retrocopy	retro_ggor_1372 ,
Macaca mulatta	ENSMMUG00000020472	1 retrocopy	retro_mmul_1719,
Monodelphis domestica	ENSMODG00000013522	1 retrocopy	retro_mdom_456,
Nomascus leucogenys	ENSNLEG00000002876	1 retrocopy	retro_nleu_1229,
Pongo abelii	ENSPPYG00000007388	2 retrocopies	retro_pabe_1260, retro_pabe_1556,
Pan troglodytes	ENSPTRG00000008155	1 retrocopy	retro_ptro_1258,