RetrogeneDB ID: retro_pabe_3243

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:6049340..6050289(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA1
• Ensembl ID: ENSPPYG00000000557
• Aliases: None
• Description: transcriptional adapter 1 [Source:RefSeq peptide;Acc:NP_001125101]

Sequence

>retro_pabe_3243
ATGGCAACTTTTGTGAGTGAGCTGGAGGTGGCCAAGAAGAACTTGAGTGAGGCCCCGGGGGACAATGTGAATCAATACTG
GGCTAACTTAAGCTGTGGTTCAAGCAGAAGATCAGCAAAGAGGACTTTGACCTTGAAACTCATAGGCTTCTTACATAGGA
TAATGTCCATTCTCACAATGATTTCTTCCTGGCCATTCTCACGCATTGTCAGATTTTGGTTTCCACACTAGAGGGTGCTG
GATCTTTGCCTGGACAGGGGGTTCTGCAGCAAAACCTGGAAAGCCCAATGGAAAGAAAAAGCTTTCTTCTGTTTGTCAGA
AATTTGATCATAGATTCCAGCCTCAAAATCCTCTCCCAAGAGCCCAGCAATTTGTGGCAAAAGATCCCCAAGATGATGAC
AACTTGAAACTTTGTTCCCACACAATGATGCTTCCCACTCAAGGCTAGCTTGAAGGGAGAATGACAGTGAATACTTATGA
GCATGGGCTGGACAATGTCACCAAGGAGGCTGTTTCAGCTCTTGTCTATGCTGTGGAGAATCACCCTAAAGATATACTGA
CATCAGTTGTGTCAAGAAGGAAAGCTTATTGGTTATGAGATGACCATTTTAAATATGCCTTTTGCAGTAATGTGACCCCA
CAGCCATACCTGAAGAATAATGTAGTAGCTTAGAACAACTTAATATAAAGCCCTCAAGCTTTTACTGCTCCCTGTGCTGG
TCAGAATCCAGCTTCTCACCCACCTCCTGATGAAGCCAAGCAGCAGACTGCATTCCTGCTGGCATGCTCTGGAGACACTC
CATCTGCATCTTTACCTCCAGTGAACATGTATGAACTTTTTGAAGTTCTGCAGATACACAAGGAAGTCATACCTTCACAT
ACTGTCTATGCCCTTAACATTGAAAGGATCATCATGAAATTCTGGCATCCAAATTATGAAGAGCTGAAG

Alignment

ORF - retro_pabe_3243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.12 %
• Parental protein coverage: 94.64 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATFVSELEAAKKNLSEALGDNVKQYWANL-KLWFKQKISKEEFDLEAHRLLTQDNVHSHNDFLLAILTR
          MATFVSELE.AKKNLSEA.GDNV.QYWANL.KLWFKQKISKE.FDLE.HRLLT.DNVHSHNDF.LAILT.
Retrocopy MATFVSELEVAKKNLSEAPGDNVNQYWANL<KLWFKQKISKEDFDLETHRLLT*DNVHSHNDFFLAILTH

Parental  CQILVSTPDGAGSLP-WPGGSAAKPGKPKGKKKLSSVRQKFDHRFQPQNPLSGAQQFVAKDPQDDDDLKL
          CQILVST..GAGSLP.W.GGSAAKPGKP.GKKKLSSV.QKFDHRFQPQNPL..AQQFVAKDPQDDD.LKL
Retrocopy CQILVSTLEGAGSLP<WTGGSAAKPGKPNGKKKLSSVCQKFDHRFQPQNPLPRAQQFVAKDPQDDDNLKL

Parental  CSHTMMLPTRGQLEGRMIVTAYEHGLDNVTEEAVSAVVYAVENHLKDILTSVVSRRKAYRLRDGHFKYAF
          CSHTMMLPT.G.LEGRM.V..YEHGLDNVT.EAVSA.VYAVENH.KDILTSVVSRRKAY.L.D.HFKYAF
Retrocopy CSHTMMLPTQG*LEGRMTVNTYEHGLDNVTKEAVSALVYAVENHPKDILTSVVSRRKAYWL*DDHFKYAF

Parental  GSNVTPQPYLKNSVVAYNNLNRNPPAFTAPCAGQNPASHPPPDDAEQQAALLLACSGDTLPASLPPVNMY
          .SNVTPQPYLKN.VVA.NNL...P.AFTAPCAGQNPASHPPPD.A.QQ.A.LLACSGDT..ASLPPVNMY
Retrocopy CSNVTPQPYLKNNVVA*NNLI*SPQAFTAPCAGQNPASHPPPDEAKQQTAFLLACSGDTPSASLPPVNMY

Parental  DPFLKLLQVHREVIPTHTVYALNIERIITKLWHPNHEELQ
          ..F...LQ.H.EVIP.HTVYALNIERII.K.WHPN.EEL.
Retrocopy ELF-EVLQIHKEVIPSHTVYALNIERIIMKFWHPNYEELK

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	0.11 RPM	8.02 RPM
SRP007412_cerebellum	0.73 RPM	8.27 RPM
SRP007412_heart	0.06 RPM	1.75 RPM
SRP007412_kidney	0.03 RPM	3.71 RPM
SRP007412_liver	0.03 RPM	1.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3243 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3243 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3928
Pan troglodytes	retro_ptro_2671
Gorilla gorilla	retro_ggor_2644

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243 ,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501,