RetrogeneDB ID: retro_ptro_20

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:62435514..62436132(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041179
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM18B1
• Ensembl ID: ENSPTRG00000007790
• Aliases: None
• Description: None

Sequence

>retro_ptro_20
ATGTTGCAGCAGGATAGTAATGATGACACTGAAGATGTTTCACTGTTTGATGCGGAAGAGGAGACGACTAATAGACCAAG
AAAAGCCAAAATCAGACATCCAGTAGCATCGTTTTTCCACTTATTCTTTCGAGTCAGTGCAATCATCGTCTATCTTCTCT
GTGAGTTGCTCAGCAGCAGCTTTATTACCTGTATGGTGACAATTATCTTGTTGTTGTCGTGTGACTTTTGGGCAGTGAAG
AATGTCACAGGTAGACTAATGGTTGGCCTACGTTGGTGGAATCACATTGATGAAGATGGAAAGAGCCATTGGGTGTTTGA
ATCTAGAAAGGAGTCCTCTCAAGAGAATAAAACTGTGTCAGAGGCTGAATCAAGAATCTTTTGGTTGGGACTTATTGCCT
GTCCAGTACTGTGGGTGATATTTGCTTTTAGTGCACTCTTCTCCTTCAGAGTAAAGTGGTTGGCGGTGGTTATTGTGGGT
GTGGTGCTACAAGGTGCCAACCTGTATGGTTACATCAGGTGCAAGGTGGGCAGCAGAAAGAATTTAACCAGCATGGCTAC
TTCATATTTTGGAAAGCAGTTTTTAAGACAAAACACTGGAGTTGATCAGACTTCCTGA

Alignment

ORF - retro_ptro_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLQQDSNDDTEDVSLFDAEEETTNRPRKAKIRHPVASFFHLFFRVSAIIVYLLCELLSSSFITCMVTIIL
          MLQQDSNDDTEDVSLFDAEEETTNRPRKAKIRHPVASFFHLFFRVSAIIVYLLCELLSSSFITCMVTIIL
Retrocopy MLQQDSNDDTEDVSLFDAEEETTNRPRKAKIRHPVASFFHLFFRVSAIIVYLLCELLSSSFITCMVTIIL

Parental  LLSCDFWAVKNVTGRLMVGLRWWNHIDEDGKSHWVFESRKESSQENKTVSEAESRIFWLGLIACPVLWVI
          LLSCDFWAVKNVTGRLMVGLRWWNHIDEDGKSHWVFESRKESSQENKTVSEAESRIFWLGLIACPVLWVI
Retrocopy LLSCDFWAVKNVTGRLMVGLRWWNHIDEDGKSHWVFESRKESSQENKTVSEAESRIFWLGLIACPVLWVI

Parental  FAFSALFSFRVKWLAVVLMGVVLQGANLYGYIRCKVGSRKNLTSMATSYFGKQFLRQNTGDDQTS
          FAFSALFSFRVKWLAVV..GVVLQGANLYGYIRCKVGSRKNLTSMATSYFGKQFLRQNTG.DQTS
Retrocopy FAFSALFSFRVKWLAVVIVGVVLQGANLYGYIRCKVGSRKNLTSMATSYFGKQFLRQNTGVDQTS

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	0.59 RPM	2.63 RPM
SRP007412_cerebellum	0.29 RPM	2.72 RPM
SRP007412_heart	0.29 RPM	2.86 RPM
SRP007412_kidney	0.76 RPM	4.58 RPM
SRP007412_liver	0.49 RPM	4.68 RPM
SRP007412_testis	0.42 RPM	8.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_20 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_20 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_20 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Homo sapiens	ENSG00000171928	1 retrocopy	retro_hsap_2278,
Homo sapiens	ENSG00000175106	1 retrocopy	retro_hsap_1625,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Microcebus murinus	ENSMICG00000015098	4 retrocopies	retro_mmur_1331, retro_mmur_151, retro_mmur_161, retro_mmur_683,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978,
Pan troglodytes	ENSPTRG00000007790	1 retrocopy	retro_ptro_20 ,
Pan troglodytes	ENSPTRG00000008796	1 retrocopy	retro_ptro_996,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000, retro_tsyr_530,