RetrogeneDB ID: retro_ggor_1239

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:42428127..42428868(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSGGOG00000012668
• Aliases: None
• Description: None

Sequence

>retro_ggor_1239
GCTGGGATCACCACCATTGAGGCGGTGAAGCGCAAGATCAAGGTTCTGCAGCAGCAGGCAGATGATGCAGAGGAGCGAGC
TGAGCGCCTCCAGCAAGAAGTTGAGGGAGAAAGGCGGGCCCGGGAACAGGCTGAGGCTGAGGTGGCCTCCTTGAACCGTA
GGATCCAGCTGATTGAAGAAGAGCTGGACCGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCAGAA
AAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACCGGGCTTTAAAAGATGAAGAAAAGATGGAACTCCA
GGAACTCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAGATAGGAAGTATGAAGAGGTGGCTCGTAAGTTGGTGA
CCATTGAAGGAGACTTGGAACGCACAGAGGAACGAGCTGAGCTGACAGAGTCCCGTTGCCGAGAGATGGATGAGCAGATT
AGACTGATGGACCAGAACCAGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATAAGAGGAAGA
AATCAAGATTTTTACTGATAAACCCAAGGAGGCAGAGACCTGTGCTGAGTTTGCTGAGCGATCGGTAGCCAAGCTGGAAA
AGACAATTGATGACTTGGAAGATAAACTGAAATGCACCAAAGAGGAGCACCTCTGTACACAAAGGATGCTGGACCAGACT
CTGCTTGACCTGAATGAGATG

Alignment

ORF - retro_ggor_1239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.97 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGIATMEEVKCNIQVLQQQADDAEERAEGLQRKV-GRKQA----EAEVASLNRRIQQVEEELDHAQEHLT
          AGI.T.E.VK..I.VLQQQADDAEERAE.LQ..V.G...A....EAEVASLNRRIQ..EEELD.AQE.L.
Retrocopy AGITTIEAVKRKIKVLQQQADDAEERAERLQQEVEGERRAREQAEAEVASLNRRIQLIEEELDRAQERLA

Parental  TALQKLEEEGKAADESERDMKVIENQALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDLE
          TALQKLEE..KAADESER.MKVIEN.ALKDEEKMELQE.QLKEAKHIAEEADRKYEEVARKLV.IEGDLE
Retrocopy TALQKLEEAEKAADESERGMKVIENRALKDEEKMELQELQLKEAKHIAEEADRKYEEVARKLVTIEGDLE

Parental  CTEERAELAESRCQETDEQIRLMDQNLKCLSDAEEKYSQKEGIYEEEIKILTDKLKEAETRAEFTERLVA
          .TEERAEL.ESRC.E.DEQIRLMDQN.KCLS.AEEKYSQKE...EEEIKI.TDK.KEAET.AEF.ER.VA
Retrocopy RTEERAELTESRCREMDEQIRLMDQNQKCLSAAEEKYSQKEDK*EEEIKIFTDKPKEAETCAEFAERSVA

Parental  KLEKTTDDLEYKLKCNKEENLCTQRMLYQTLLDLNEM
          KLEKT.DDLE.KLKC.KEE.LCTQRML.QTLLDLNEM
Retrocopy KLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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	4.22 RPM	0.05 RPM
SRP007412_cerebellum	1.54 RPM	0.04 RPM
SRP007412_heart	1.16 RPM	0.06 RPM
SRP007412_kidney	4.95 RPM	0.41 RPM
SRP007412_liver	1.69 RPM	0.05 RPM
SRP007412_testis	5.80 RPM	0.21 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_1239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1239 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
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,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921, retro_nleu_922,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318, retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,