RetrogeneDB ID: retro_ggor_1843

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:38157510..38157801(+)
• Located in intron of: ENSGGOG00000001784

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D4
• Ensembl ID: ENSGGOG00000003378
• Aliases: None
• Description: None

Sequence

>retro_ggor_1843
ATGGCACTAAGACAGATTAATAAGGAACTTAGTGATTTGGCCCATGACCCTCCAGCACAATGTTCTGCAGGTCCAGTTGA
GGATGGTATGTTTCATTGGCAAGCCACAATTATGGGACCTAATGACAGCCCATATCAAAGCGGTGTATTCTTTTTGACAA
TTCATTTTCCTACAGACTGCTCCTTCAAACCACCTAAGGTTGCATGTACAACAAGGATTTATCATCCAACTATTAACAGT
AATGGCAGCATTTGTCTCGATATTCTAAGATCACAGTGGTTGCCTGCTTTA

Alignment

ORF - retro_ggor_1843 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.51 %
• Parental protein coverage: 65.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALKRIQKELTDLQRDPPAQCSAGPVGDDLFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFT
          MAL..I.KEL.DL..DPPAQCSAGPV.D..FHWQATIMGPNDSPYQ.GVFFLTIHFPTD..FKPPKVA.T
Retrocopy MALRQINKELSDLAHDPPAQCSAGPVEDGMFHWQATIMGPNDSPYQSGVFFLTIHFPTDCSFKPPKVACT

Parental  TKIYHPNINSNGSICLDILRSQWSPAL
          T.IYHP.INSNGSICLDILRSQW.PAL
Retrocopy TRIYHPTINSNGSICLDILRSQWLPAL

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	0.19 RPM	28.01 RPM
SRP007412_cerebellum	0.28 RPM	24.62 RPM
SRP007412_heart	0.13 RPM	10.57 RPM
SRP007412_kidney	0.41 RPM	23.96 RPM
SRP007412_liver	0.11 RPM	17.01 RPM
SRP007412_testis	1.86 RPM	17.92 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_1843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1843 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2330

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003997	1 retrocopy	retro_btau_1261,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843 , retro_ggor_2936, retro_ggor_436,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Gorilla gorilla	ENSGGOG00000010832	1 retrocopy	retro_ggor_953,
Gorilla gorilla	ENSGGOG00000028073	3 retrocopies	retro_ggor_1425, retro_ggor_861, retro_ggor_924,
Myotis lucifugus	ENSMLUG00000011919	3 retrocopies	retro_mluc_1826, retro_mluc_1827, retro_mluc_594,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Nomascus leucogenys	ENSNLEG00000003364	3 retrocopies	retro_nleu_54, retro_nleu_876, retro_nleu_90,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Tupaia belangeri	ENSTBEG00000003691	9 retrocopies	retro_tbel_1273, retro_tbel_2535, retro_tbel_2782, retro_tbel_307, retro_tbel_367, retro_tbel_37, retro_tbel_4118, retro_tbel_4163, retro_tbel_4312,
Tarsius syrichta	ENSTSYG00000000595	14 retrocopies	retro_tsyr_1007, retro_tsyr_1145, retro_tsyr_1162, retro_tsyr_1314, retro_tsyr_1392, retro_tsyr_1415, retro_tsyr_1677, retro_tsyr_1694, retro_tsyr_1859, retro_tsyr_683, retro_tsyr_789, retro_tsyr_836, retro_tsyr_838, retro_tsyr_919,