RetrogeneDB ID: retro_ptro_1528

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:11416320..11417237(+)
• Located in intron of: ENSPTRG00000011658

Retrocopy information

• Ensembl ID: ENSPTRG00000040789
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AIDA
• Ensembl ID: ENSPTRG00000002010
• Aliases: None
• Description: None

Sequence

>retro_ptro_1528
ATGTCAGAGGTGACCCAGAGTCTGCTGCAGCGCTGGGGCGCCAGTTTTAGGAGAGGCGCCGACTGCGACTCTTGGGGCCA
GCTGGTGAGGCGATAGACAAGTATCAGATATTAGCAAGACATCTACAAAAAGAGGCCCAAGCTCAACACAATAATTCTGA
ATTCACAGAAGAACAAAAGAAAACCATAGGCAAAATTGCAACATGCTTAGAATTGCGAAGTACAGCTTTACAGTCCACAC
AGTCTCAAGAAGAATTTAAATTGGAGAACCTGAAGAAGCTAGAACCAATCCTAAAGAATATTCTTACATATAATAAAGAA
TTCCCATTTGATGTTTAGCCTGTCCCATTAAGAAGAATTTTGGCACCTGGTGAAGAAGAGAATTTGGAATTTGAAGAAGA
TGAAGAAGAGGGTGGTGCTGGAGCAGGGTCTCCTGATTCTTTTCCTGCTAGAGTTCCCGGTACTTTCTTACCAAGGTTGC
CATTGGAACCAGGAATGACATTACTCACTATCAGAATTGAGAAAACTGGTTTGAAAGATGCTGGGCAGTGCATCAATCCC
TGTATTACAGTTAGTGTAAAGGATCTGAATGGCATAGACTTAACTCCTGTGCAAGATACTCCTGTGGCTTCAAGAAAAGA
AGATACATATGTTCATTTTAATGTGGACATTGAGCTCCAGAAGCATGTTGAAAAATTAACCAAAGGTGCAGCTATCTTCT
TTGAATTCAAACACTACAAGCCTAAAAAAAGGTTTACCAGCACCAAGTGTTTTGCTTTCATGGAGATGGATGAAATTAAA
CTTGGGCCAATTGTAATAGAACTATACAAGAAACCCACTGACTTTAAAAAAAAGCAATTGCAATTATTGACCAAGAAACC
ACTTTATCTTCATCTACATCAAACTTTGCACAAGGAA

Alignment

ORF - retro_ptro_1528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSEVTRSLLQRWGASFRRGADFDSWGQLV-EAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATC
          MSEVT.SLLQRWGASFRRGAD.DSWGQLV.EAID.YQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATC
Retrocopy MSEVTQSLLQRWGASFRRGADCDSWGQLV<EAIDKYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATC

Parental  LELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGEEENLEFEEDEEEGG
          LELRS.ALQSTQSQEEFKLE.LKKLEPILKNILTYNKEFPFDV.PVPLRRILAPGEEENLEFEEDEEEGG
Retrocopy LELRSTALQSTQSQEEFKLENLKKLEPILKNILTYNKEFPFDV*PVPLRRILAPGEEENLEFEEDEEEGG

Parental  AGAGSPDSFPARVPGTLLPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPV
          AGAGSPDSFPARVPGT.LPRLP.EPGMTLLTIRIEK.GLKDAGQCI.P.ITVSVKDLNGIDLTPVQDTPV
Retrocopy AGAGSPDSFPARVPGTFLPRLPLEPGMTLLTIRIEKTGLKDAGQCINPCITVSVKDLNGIDLTPVQDTPV

Parental  ASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKP
          ASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIK.GPIVIELYKKP
Retrocopy ASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKLGPIVIELYKKP

Parental  TDFKRKKLQLLTKKPLYLHLHQTLHKE
          TDF....LQLLTKKPLYLHLHQTLHKE
Retrocopy TDFXXXQLQLLTKKPLYLHLHQTLHKE

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	0.20 RPM	34.89 RPM
SRP007412_cerebellum	0.00 RPM	38.47 RPM
SRP007412_heart	0.03 RPM	51.79 RPM
SRP007412_kidney	0.03 RPM	42.60 RPM
SRP007412_liver	0.00 RPM	40.56 RPM
SRP007412_testis	0.00 RPM	131.52 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1528 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1528 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2076
Gorilla gorilla	retro_ggor_1627
Pongo abelii	retro_pabe_2015

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007593	2 retrocopies	retro_btau_1163, retro_btau_573,
Choloepus hoffmanni	ENSCHOG00000010095	2 retrocopies	retro_chof_1919, retro_chof_97,
Dasypus novemcinctus	ENSDNOG00000008380	5 retrocopies	retro_dnov_1765, retro_dnov_1909, retro_dnov_1961, retro_dnov_2172, retro_dnov_2280,
Homo sapiens	ENSG00000186063	4 retrocopies	retro_hsap_1901, retro_hsap_2076, retro_hsap_2998, retro_hsap_410,
Gorilla gorilla	ENSGGOG00000015289	3 retrocopies	retro_ggor_1394, retro_ggor_1627, retro_ggor_2077,
Macaca mulatta	ENSMMUG00000015025	1 retrocopy	retro_mmul_1918,
Monodelphis domestica	ENSMODG00000004774	3 retrocopies	retro_mdom_1417, retro_mdom_1418, retro_mdom_1448,
Nomascus leucogenys	ENSNLEG00000013583	1 retrocopy	retro_nleu_748,
Oryctolagus cuniculus	ENSOCUG00000017030	1 retrocopy	retro_ocun_688,
Pongo abelii	ENSPPYG00000000196	2 retrocopies	retro_pabe_2015, retro_pabe_2485,
Pan troglodytes	ENSPTRG00000002010	3 retrocopies	retro_ptro_1254, retro_ptro_1528 , retro_ptro_2027,
Tarsius syrichta	ENSTSYG00000005745	3 retrocopies	retro_tsyr_101, retro_tsyr_1795, retro_tsyr_514,
Tursiops truncatus	ENSTTRG00000016594	1 retrocopy	retro_ttru_1084,