RetrogeneDB ID: retro_ggor_335

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:189222713..189223885(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFDP1
• Ensembl ID: ENSGGOG00000004908
• Aliases: None
• Description: None

Sequence

>retro_ggor_335
ATGGCAAAAGTTGCTGGTCTAATTGAAGCAAACGGAGAACTCAAGGTCTTCATAGACCAGAACCTTAGTCCCGGAAAAGG
CATTGGTGTCCCTCATGGCCGTTCACCCCTCCATCGTCAGCCCGCTCGGGAAGCAGCTCTTGCCGAAAACCTTTGGACAG
TCCAATATCAACGTTGTCCCGCAAGTGGTAACCGGTACGCCTCAGAGACCGGCAGCGTCAAACACCCTCGTGATAGGTAG
CCCACACACCGCCAGCACTCACTTTGCCTCTCAGAACCAGCCTTCCGACTCCTCACCTTGGTCTGCCGGGAAGTGCAACA
GGAAAGGAGAGAAGAATGGCAAGGCCTGTGGCATTTCTCCAGGAAGGTCTGAGACAAGGTGCAGTGGAAAGGGACCACTT
CCTATCACGAGGTGGCGGACGAGCTGGCAGAGGAATTCAGTGCTGCCAGCAACCACATCTTACCAAGCGAGTCAGCTTAT
GACCAGAGCAACATCGACGGCGCGTCTACTATGCCTTAAACGTGCTGATGGCCATGAATATCTCCAAGGAGAAGAAGGAG
ATCAAGTGAGTTGGTCTGCCCACCAACTCGGCTCAGGAATGTCAGAACTCAGAGGTGGAAAGACAGAGGAGACTTGACAG
AATAAAACAGAAAATCTCAATTTCAGAAACTTATTTGACAGTAAATTGCCTTCAAGAACCTGGTGAAGAGAGAAACCAGC
ACGCGGAGCAGCAGGCCAGCCAGCCAACGACGCCCAGCTGGCTCATCCACCTGCCCTTCATCATCGTTAACACCAGCAAG
AAGACCGTCATCGACTGCAGCATCTCCAACGACAAATTCGAGTATCTGTTTAATTTTGACAACACATCTGAAATCTACAA
TGACATAGAAGTGCTGAAGCGGATGAGCATGGCTTGTGGGCTGGAGTCCGGGAGCTTCTCTGCTGAGGACCTTAAAATGG
CCAGAAGTCTGGTCCCAAAGGCTCTGGAGCCGTACGTGACAGAAATGGCTCAGGGAACTGTCGGAGGCGTGTTCATCACG
ACGGCACGTTCCATGTCTAACGGCAAGAAGCTCTCTGCCAGTGACCTGACCAATGGTGTGGATGAGATACTGGCCACAAG
CTCCAACCTCAGTACAATGGCTCCGGGGCGGAGGCCCCGGTGTCCTACGTCG

Alignment

ORF - retro_ggor_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 98.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAKDAGLIEANGELKVFIDQNLSPGKGV-VSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQR
          MAK.AGLIEANGELKVFIDQNLSPGKG..VSL.AVHPS.V.PLGKQLLPKTFGQSN.N...QVV.GTPQR
Retrocopy MAKVAGLIEANGELKVFIDQNLSPGKGI>VSLMAVHPSIVSPLGKQLLPKTFGQSNINVVPQVVTGTPQR

Parental  PAASNTLVVGSPHTPSTHFASQNQPSDSSPWSAGKRNRKGEKNGK-GLRHFSMKVCEKVQRKGTTSYNEV
          PAASNTLV.GSPHT.STHFASQNQPSDSSPWSAGK.NRKGEKNGK.GL.HFS.KV..KVQ.KGTTSY.EV
Retrocopy PAASNTLVIGSPHTASTHFASQNQPSDSSPWSAGKCNRKGEKNGK<GLWHFSRKV*DKVQWKGTTSYHEV

Parental  ADELVAEFSAADNHILPNESAYDQKNI-RRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEV
          ADEL..EFSAA.NHILP.ESAYDQ.NI.RRRVY.ALNVLMAMNI.SKEKKEIK..GLPTNSAQECQN.EV
Retrocopy ADELAEEFSAASNHILPSESAYDQSNI<RRRVYYALNVLMAMNI-SKEKKEIK*VGLPTNSAQECQNSEV

Parental  ERQRRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSIS
          ERQRRL.RIKQK.S.................RN.HAEQQAS.P..P...IHLPFIIVNTSKKTVIDCSIS
Retrocopy ERQRRLDRIKQKISISETYLTVNCLQEPGEERNQHAEQQASQPTTPSWLIHLPFIIVNTSKKTVIDCSIS

Parental  NDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFI
          NDKFEYLFNFDNT.EI..DIEVLKRM.MACGLESGS.SAEDLKMARSLVPKALEPYVTEMAQGTVGGVFI
Retrocopy NDKFEYLFNFDNTSEIYNDIEVLKRMSMACGLESGSFSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFI

Parental  TTAGSTSNGTRFSASDLTNGADGMLATSSNGSQYS-GSRVETPVS
          TTA.S.SNG...SASDLTNG.D..LATSSN.S....G.R...P.S
Retrocopy TTARSMSNGKKLSASDLTNGVDEILATSSNLSTMAPGRRPRCPTS

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	23.69 RPM
SRP007412_cerebellum	0.04 RPM	35.18 RPM
SRP007412_heart	0.00 RPM	6.91 RPM
SRP007412_kidney	0.00 RPM	17.09 RPM
SRP007412_liver	0.00 RPM	11.71 RPM
SRP007412_testis	9.12 RPM	46.21 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_335 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_299
Pongo abelii	retro_pabe_378

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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,