RetrogeneDB ID: retro_ggor_1836

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:28455234..28455620(+)
• 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_1836
GAAGAGGCTGACCGCAAATACGAGGAGGTAGCTCGTAAGCTGGTCATCCTGGAGGGTGAGCTGGAGAGGGCAGAGGAGCG
TGCGGAGGTGTCTGAACTAAAATGTGGTGACGTTGAAGAAGAACTCAAGAATGTTAGTAACAATGTGAAATCTCTGGAGG
CTGCATCTGAAAAGTATTCTGAAAAGGAGGACAATGTGAAGAAGAAATTAAACTTCTGTGTGACAAACTGAAAGAGGATG
AGACCCGTGCTGAATGTGCAGAGAGAGCGGTCGCAAATCTGGAAAAGACAATGGATGACCTGGAAGAGTATCTTGTTCAG
GCCAAAGAAGAGAACGTGGGCTTACATCAGACACTGGATCAGACACTAAACGAAGTTAACTGTATA

Alignment

ORF - retro_ggor_1836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.62 %
• Parental protein coverage: 52.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEADRKYEEVARKLVILEGELERAEERAEVSELKCGDLEEELKNVTNNLKSLEAASEKYSEKED-KYEEE
          EEADRKYEEVARKLVILEGELERAEERAEVSELKCGD.EEELKNV.NN.KSLEAASEKYSEKED...EEE
Retrocopy EEADRKYEEVARKLVILEGELERAEERAEVSELKCGDVEEELKNVSNNVKSLEAASEKYSEKED<QCEEE

Parental  IKLLSDKLKEAETRAEFAERTVAKLEKTIDDLEDELYAQKLKYKAISEELDHALNDMTSL
          IKLL.DKLKE.ETRAE.AER.VA.LEKT.DDLE..L...K.........LD..LN.....
Retrocopy IKLLCDKLKEDETRAECAERAVANLEKTMDDLEEYLVQAKEENVGLHQTLDQTLNEVNCI

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	0.58 RPM	39.56 RPM
SRP007412_cerebellum	0.39 RPM	70.96 RPM
SRP007412_heart	0.28 RPM	22.20 RPM
SRP007412_kidney	0.49 RPM	21.75 RPM
SRP007412_liver	0.66 RPM	20.60 RPM
SRP007412_testis	4.35 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_1836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1836 has 0 orthologous retrocopies within eutheria group .

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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,