RetrogeneDB ID: retro_ggor_609

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:113590975..113591568(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM4
• Ensembl ID: ENSGGOG00000014510
• Aliases: None
• Description: None

Sequence

>retro_ggor_609
GGCGCTGTGGCTGTCCTCAACTGACGCATCCAGCTTGTTAAGGAGGAGTTGGACGGGGCTCGGGAACGACTGGTCACGGC
CCTGCAGAAGCTAGAGGAGGGGGAAAAGGCTGCAGATGAGCGTGAGAGAGAATGAAGGTGATAGAAAACCGGGCTATGAG
GGATGAGGAGAAGATGGATTCGGGAGATGCAGCTCAAAGAGGCCAAGCACACTGCGGCCGGAGGCTGACCGCAAATAAGA
GGAGGTAGCTCGGAAACTGGCCATCACGGAGGGCGAACTGGCCAGAGCAGAGGAGCGTGCAGAGGTGTCTGAACTAAAAT
GTGGTGACCTGGCAGAAGAACTCAAGAATGTCACTAACAATCTGAAACCGCCGGAGGCTGCATTGAAAAGTATTCTGACA
AGGAGGACAAATATGAAGAAAAAATTAAACTTCTGTCTGACAACTGAAGGAGGCTGAGATCCGTGCTGAATTTGCAGAGA
TAATGGTTGCAAAACTGGAAAAGACAACTGATGACCTGGAAGAGAAATTTGCCCAGGCCAAAGAAGAGGGCGCGGGCTTA
TATCAGACACTGGATCAGGCACTAAATGAACTT

Alignment

ORF - retro_ggor_609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.46 %
• Parental protein coverage: 80.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GDVAALNRRIQLVEEELDRAQERLATALQKLEEAEKAADESER-GMKVIENRAMKDEEKMEIQEMQLKEA
          G.VA.LN.RIQLV.EELD.A.ERL.TALQKLEE.EKAADE.ER..MKVIENRAM.DEEKM..........
Retrocopy GAVAVLN*RIQLVKEELDGARERLVTALQKLEEGEKAADERER<RMKVIENRAMRDEEKMDSGDAAQRGQ

Parental  KH-IAEEADRKYEEVARKLVILEGELERAEERAEVSELKCGDLEEELKNVTNNLKSLEAA-SEKYSEKED
          .H....EADRK.EEVARKL.I.EGEL.RAEERAEVSELKCGDL.EELKNVTNNLK..EAA..EKYS.KED
Retrocopy AH<LRPEADRK*EEVARKLAITEGELARAEERAEVSELKCGDLAEELKNVTNNLKPPEAA<IEKYSDKED

Parental  KYEEEIKLLSD-KLKEAETRAEFAERTVAKLEKTIDDLEDELYAQKLKYKAISEELDHALNDM
          KYEE.IKLLSD..LKEAE.RAEFAE..VAKLEKT.DDLE......K.........LD.ALN..
Retrocopy KYEEKIKLLSD<QLKEAEIRAEFAEIMVAKLEKTTDDLEEKFAQAKEEGAGLYQTLDQALNEL

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	39.56 RPM
SRP007412_cerebellum	0.00 RPM	70.96 RPM
SRP007412_heart	0.00 RPM	22.20 RPM
SRP007412_kidney	0.00 RPM	21.75 RPM
SRP007412_liver	0.16 RPM	20.60 RPM
SRP007412_testis	0.10 RPM	113.34 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_609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_609 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_624
Callithrix jacchus	retro_cjac_206

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004553	2 retrocopies	retro_btau_1604, retro_btau_1758,
Canis familiaris	ENSCAFG00000015796	1 retrocopy	retro_cfam_2107,
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206,
Homo sapiens	ENSG00000167460	2 retrocopies	retro_hsap_2623, retro_hsap_3969,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Gorilla gorilla	ENSGGOG00000014510	4 retrocopies	retro_ggor_1836, retro_ggor_2665, retro_ggor_2801, retro_ggor_609 ,
Monodelphis domestica	ENSMODG00000014882	1 retrocopy	retro_mdom_1354,
Mus musculus	ENSMUSG00000031799	1 retrocopy	retro_mmus_1625,
Nomascus leucogenys	ENSNLEG00000005413	2 retrocopies	retro_nleu_1952, retro_nleu_469,
Oryctolagus cuniculus	ENSOCUG00000009884	1 retrocopy	retro_ocun_1652,
Pan troglodytes	ENSPTRG00000010637	10 retrocopies	retro_ptro_1002, retro_ptro_1109, retro_ptro_1341, retro_ptro_1342, retro_ptro_1750, retro_ptro_1768, retro_ptro_2648, retro_ptro_2694, retro_ptro_2830, retro_ptro_516,
Pteropus vampyrus	ENSPVAG00000009755	2 retrocopies	retro_pvam_186, retro_pvam_187,
Ictidomys tridecemlineatus	ENSSTOG00000024252	1 retrocopy	retro_itri_1858,
Tupaia belangeri	ENSTBEG00000012927	7 retrocopies	retro_tbel_1435, retro_tbel_2468, retro_tbel_3663, retro_tbel_3709, retro_tbel_3872, retro_tbel_4651, retro_tbel_482,
Tarsius syrichta	ENSTSYG00000010642	9 retrocopies	retro_tsyr_1377, retro_tsyr_1613, retro_tsyr_1642, retro_tsyr_1853, retro_tsyr_628, retro_tsyr_694, retro_tsyr_704, retro_tsyr_742, retro_tsyr_749,
Tursiops truncatus	ENSTTRG00000014542	2 retrocopies	retro_ttru_504, retro_ttru_839,