RetrogeneDB ID: retro_pabe_378

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:40892891..40893550(-)
• 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_378
ATGGCAAAAGTTGCCGGTCTAATTGAAGCCAACGGAGAACTCAAGGTCTTCATAGACCAGAACCTTAGTCCCGGAAAAGG
CATTGGTGTCCCTCGTGGCCGTTCACCCCTCCATCGTCAACCCGCTCGGGAAGCAGCTCTTGCCGAAAACCTTTGGACAG
TCCAATGTCAGCATTGTCCGGCAAGTGGTAACCGGTACGCCTCAGAGACCGGCAGCGTCAAACGCCCTCGTGATAGGTAG
CCCACACACCGCCAGCACTCACTTTGCCTCTCAGAACCAACCTTCCGACTCCTCACCTTGGTCTGCGGGGAAGCGCAACA
GGAAAGGAGAGAAGAATGGCAAGCCCTGTAGCATTTCTCCAGGAAGGTCTGAGACAAGGTGCAGTGGAAAATGACCACTT
CCTACCACGAAGTGGCGGACGAGCTGGTAGCGGAATTCAGTGCTGCCGGCAACCACATCTTACCAAGCGAGTCAGCTTAT
GACCAGAGGAACATCGACGATGCGTCTACGATGCCTTAAACGTGCTGATGGCCATGAACATCTCCAAGGAGAAGAAGGAG
ATCAAGTGAGTTCGTCTGCCCGCCAACTCGGCTCGGGAATGTCAGAACTGAGAGGTGGAAAGACAGAGGAGACTTGACAG
AATAAAACAGAAAATCTCA

Alignment

ORF - retro_pabe_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.82 %
• Parental protein coverage: 53.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAKDAGLIEANGELKVFIDQNLSPGKGV-VSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQR
          MAK.AGLIEANGELKVFIDQNLSPGKG..VSLVAVHPS.VNPLGKQLLPKTFGQSNV.I..QVV.GTPQR
Retrocopy MAKVAGLIEANGELKVFIDQNLSPGKGI>VSLVAVHPSIVNPLGKQLLPKTFGQSNVSIVRQVVTGTPQR

Parental  PAASNTLVVGSPHTPSTHFASQNQPSDSSPWSAGKRNRKGEKNGK-GLRHFSMKVCEKVQRKGTTSYNEV
          PAASN.LV.GSPHT.STHFASQNQPSDSSPWSAGKRNRKGEKNGK..L.HFS.KV..KVQ.K.TTSY.EV
Retrocopy PAASNALVIGSPHTASTHFASQNQPSDSSPWSAGKRNRKGEKNGK<AL*HFSRKV*DKVQWKMTTSYHEV

Parental  ADELVAEFSAADNHILPNESAYDQKNI-RRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEV
          ADELVAEFSAA.NHILP.ESAYDQ.NI.RR.VYDALNVLMAMN.ISKEKKEIK...LP.NSA.ECQN.EV
Retrocopy ADELVAEFSAAGNHILPSESAYDQRNI<RRCVYDALNVLMAMN-ISKEKKEIK*VRLPANSARECQN*EV

Parental  ERQRRLERIKQKQS
          ERQRRL.RIKQK.S
Retrocopy ERQRRLDRIKQKIS

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	0.00 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	0.00 RPM	11.23 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_378 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_378 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_299
Gorilla gorilla	retro_ggor_335

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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 ,