RetrogeneDB ID: retro_ptro_2027

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:161355368..161356284(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

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

Sequence

>retro_ptro_2027
ATGTCGGAGGTGACCTGGAGTCTGCTGCAGCTCTGGGGCGCCAGTTTTAGGAGAGGCGCCAACTTCGACTTTTGGGGCCA
GCTGGTGGAGGCGATAGATGAGTATTAGATATTAGCAAGACATCTACAAAAAGAGGCCCAAGCTCAACACAATAATTCTG
AATTCACAGAAGAACAAAAGAAAACCATAGGCAAAATTGCAACATGCTTAGAATTGTGAAGTGCAGCTTTACAGTCCACA
CAGTCTCAAGAAGAATTTAAACTGGAGGACCTGAAGAAGCTAGAACCAATCCTAAAGAATATTCTTACATATAATAAAGA
ATTCCCATTTGATATTCAGCCTGTCCCATTAAGAAGAATTTTGGCACCTGGTAAAGAGGAGAATTTGGAATTTGAAGAAG
AAGAAGCGGGTGGTGCTGGAGCAGGGTCTCCTGATTCTTTTCCTGCTAGAGTTCCCGATGCTTTAGATACCAAGGTTGCC
ATTGGAACCAGGAATGACATTACTCACTATCAGAATTGAGAAAATTGGTTTGAAAGATGCTGGGCAGTGCATCGATCCCT
ATATTACAGTTAGAGTAAAGGATCTGAATGGCATAGACTGAACTCCTGTGCAAGATACTCCTGTGGCTTCAAGAAAAGAA
GATACATATCTTCATTTTAATGTGGACATTGAGCTCCAGAAGCATGTTGAAAAAGTAATCAAAGGTGCAGCTATCTTCTT
TGAATTCAAACACCAGAAGCCTAAAAAAAGGTTTACCAGCACCAAGTGTTTTGCTTTCATGGAGATGGATGAAATTAAAC
CTGGGCCAATTGTAATAGAACTATACAAGAAACCCACTGACTTTAAAAGAAAGAAATTGCAATTATTGACGAAGAAAACA
CTTTATCTTCGTCTACATCAAACTTTGCACAAGGAA

Alignment

ORF - retro_ptro_2027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSEVTRSLLQRWGASFRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL
          MSEVT.SLLQ.WGASFRRGA.FD.WGQLVEAIDEY.ILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL
Retrocopy MSEVTWSLLQLWGASFRRGANFDFWGQLVEAIDEY*ILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL

Parental  ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGEEENLEFEEDEEEGGA
          EL.SAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFD.QPVPLRRILAPG.EENLEFEE.EE.GGA
Retrocopy EL*SAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDIQPVPLRRILAPGKEENLEFEE-EEAGGA

Parental  GAGSPDSFPARVPGTL-LPRLPSEPGMTLLTIRIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPV
          GAGSPDSFPARVP..L..PRLP.EPGMTLLTIRIEKIGLKDAGQCIDPYITV.VKDLNGID.TPVQDTPV
Retrocopy GAGSPDSFPARVPDAL>IPRLPLEPGMTLLTIRIEKIGLKDAGQCIDPYITVRVKDLNGID*TPVQDTPV

Parental  ASRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKP
          ASRKEDTY.HFNVDIELQKHVEK..KGAAIFFEFKH.KPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKP
Retrocopy ASRKEDTYLHFNVDIELQKHVEKVIKGAAIFFEFKHQKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKP

Parental  TDFKRKKLQLLTKKPLYLHLHQTLHKE
          TDFKRKKLQLLTKK.LYL.LHQTLHKE
Retrocopy TDFKRKKLQLLTKKTLYLRLHQTLHKE

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	0.36 RPM	34.89 RPM
SRP007412_cerebellum	0.00 RPM	38.47 RPM
SRP007412_heart	0.12 RPM	51.79 RPM
SRP007412_kidney	0.00 RPM	42.60 RPM
SRP007412_liver	0.00 RPM	40.56 RPM
SRP007412_testis	0.21 RPM	131.52 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2027 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2027 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2998
Gorilla gorilla	retro_ggor_2077
Pongo abelii	retro_pabe_2485
Macaca mulatta	retro_mmul_1918

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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,