RetrogeneDB ID: retro_pabe_1314

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:77049291..77050520(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFDP1
• Ensembl ID: ENSPPYG00000025889
• Aliases: None
• Description: transcription factor Dp-1 [Source:HGNC Symbol;Acc:11749]

Sequence

>retro_pabe_1314
ATGGCAAAAGATGCCGGTCTAATTGAAGCCAACGGAGAACTCAAGATCTTCATAGACCAGAATCTTAGTCCCGGAAAAGG
CGTGGTGTCCCTCGTGGCCGTTCACTCCTCCACTGTCAACCCGCTCGGGGAGCAGCTCTTGGCAACAACCTTTGAACAGT
CCAATGTCAACATTGCCCAGCAAGTGGTAATTGGTGCGCCTCAGAGACGGGCAGCGTCAAACGCCTTGGGGGTAGGAAGC
CCACACACCCCCAGCACTCACTTTGCCGCTCAGAACCAGCCTTCCTACTCCTCACCTTGGTCTGCCGGGAAGCGCAACAG
AAAAGGAGAGAAGAATGGCAGGGGCCTGCGGCATTTCTCCATGAAGGTCTGCGAGAAGGTGCAGAGGAAAGGGACCGCTT
CCTACAACGAAGCGGCAGACGAGCTGGTCGCGGAGTTCAGTGCTGCCGACAACCACATCTTACCAAACGAGTCAGCTTAT
GACCAGAAGAACATAAGACGGCGCGTCTACGATGCCTTAAACGTGCTGATGGCCGTGAACATCATCTCCAAGGAGAAAAA
GGAGGTCAAGTGGATTGGTCTGCCCACCAACTCGGCATAGGAATGTCAGAACTTAGAGGTGGAAAGACAGAGGAGACTTG
AAAGAATAAAACAGAAACAGTCTCAACTTCAAAACTTATTCTACAGCAAATTACCTTCAAGAAACTGGTGCAGAGAAACC
GGCACGCGGAGCAGTAGGCCAGCCAGCCGCCGCCAGCCAACTCGGTCATCCACCTGCCCTTCATCATCATCAACACCAGC
AAGCAGACGGTCATCGACTGCAGCATCTCCAACGACAAATTCGAGTATCTATTTAATTTTGACAACACATTTGAAATCCA
CGATGACATAGAAGTGCTGAAGCGGATGGGCATGCCCTACGGGCTGGAGTCCAGGAGCTGCTCTGCTGAAGACTTTAAAA
TGGCCAGAAGTCTGGTCCCAAAGACTCTGGAGCCGTACGTGACAGAAATGGCTCAGGGAACTGTTGGAGGCGTGTTCATC
GCGACGGCAGGTTCCACGTCTAACGGCACGAGGTTCTCTGCCAGTGACCTGACCAATGGTGCAGATGGGATACTGGCCAC
AAGTTCTAATGGGTCTCAGTACAGCAGCTCCAGGGTGGAGACCCCGGTGTATTACGTCAGGGAGGACGACGAGGAGGATA
ATGACTTCAACGAGAATGAGGAGGACGAC

Alignment

ORF - retro_pabe_1314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKDAGLIEANGELKVFIDQNLSPGKGVVSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQRP
          MAKDAGLIEANGELK.FIDQNLSPGKGVVSLVAVH.STVNPLG.QLL..TF.QSNVNIAQQVVIG.PQR.
Retrocopy MAKDAGLIEANGELKIFIDQNLSPGKGVVSLVAVHSSTVNPLGEQLLATTFEQSNVNIAQQVVIGAPQRR

Parental  AASNTLVVGSPHTPSTHFASQNQPSDSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGTTSYNEVAD
          AASN.L.VGSPHTPSTHFA.QNQPS.SSPWSAGKRNRKGEKNG.GLRHFSMKVCEKVQRKGT.SYNE.AD
Retrocopy AASNALGVGSPHTPSTHFAAQNQPSYSSPWSAGKRNRKGEKNGRGLRHFSMKVCEKVQRKGTASYNEAAD

Parental  ELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQ
          ELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMA.NIISKEKKE.KWIGLPTNSA.ECQNLEVERQ
Retrocopy ELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAVNIISKEKKEVKWIGLPTNSA*ECQNLEVERQ

Parental  RRLERIKQKQSQLQ-ELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISND
          RRLERIKQKQSQLQ..LILQQI.FK.LVQRNRHAEQ.AS.PPP.NSVIHLPFII.NTSK.TVIDCSISND
Retrocopy RRLERIKQKQSQLQ<KLILQQITFKKLVQRNRHAEQ*ASQPPPANSVIHLPFIIINTSKQTVIDCSISND

Parental  KFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFITT
          KFEYLFNFDNTFEIHDDIEVLKRMGM..GLES.SCSAED.KMARSLVPK.LEPYVTEMAQGTVGGVFI.T
Retrocopy KFEYLFNFDNTFEIHDDIEVLKRMGMPYGLESRSCSAEDFKMARSLVPKTLEPYVTEMAQGTVGGVFIAT

Parental  AGSTSNGTRFSASDLTNGADGMLATSSNGSQYSGSRVETPVSYVGEDDEEDDDFNENDEDD
          AGSTSNGTRFSASDLTNGADG.LATSSNGSQYS.SRVETPV.YV.EDDEED.DFNEN.EDD
Retrocopy AGSTSNGTRFSASDLTNGADGILATSSNGSQYSSSRVETPVYYVREDDEEDNDFNENEEDD

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	0.06 RPM	20.68 RPM
SRP007412_cerebellum	0.00 RPM	34.05 RPM
SRP007412_heart	0.00 RPM	16.50 RPM
SRP007412_kidney	0.00 RPM	21.74 RPM
SRP007412_liver	0.03 RPM	11.23 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1314 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1314 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314 , retro_pabe_132, retro_pabe_378,