RetrogeneDB ID: retro_ggor_390

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:52907731..52908584(-)
• Located in intron of: ENSGGOG00000004919

Retrocopy information

• Ensembl ID: ENSGGOG00000025934
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSGGOG00000009371
• Aliases: None
• Description: None

Sequence

>retro_ggor_390
ATGGTGGATGACACCAGTGCAGTGGGGGGGCCTGGAGGCCCTGGCGGCCCTGGGATGGGGAACTGCGGTGGCTTCCGCGG
AGGTTTCGGCAGTGGCATCCGGGGCCGGGGCCGAGGCCGCGGAGCTCGCGGAGGCAAGGCCGAGGATAAGGAGTGGATGC
CCGTCACCAAGCTGGGCTGCTTGGTCAAGGACATGAAGATCAAGTCCCGGGAGGAGATCTATCTCTTCTCCCTGCCCATT
AAGGAATCAGATCATTGACTTTTTCCTGGGGGCCTCTCTCAAGGATGAGGTTTTGAAGATTATGCCAGTGCAGACGCAGA
CCCGTGCTGGCCAGCGCACCAGGTTCAAGGCGTTTGTTGCTATCGGGGACTACAATGGCCACGTCGGTCTGGGTGTTAAG
TGCTCCAAGGAGGTGGCCACCGCCATCCATGGGGCCATCATCCTGGCCAAGCTCTCCATTGTCCCCGTGCGCAGAGGCTA
CTGGGGGAACAAGATTGGCAAGCCCCACACCGTCCCTTGCAAGGTGACAGGCCGCTGCAGCTCTGCGCTGGTGCACCTCA
TCCCGGTACCCAGGGGCACTGGCATTGTCTCCGCACCTGTGCCCAAGAAGCTGCTCATGATGGCTGGTATCAATGACTGC
TACACCTCAGCCTGGGGCTGCACTGCCACCCTGGGCAACTTCGCCAAGGCCACCTTTGATGCCATTTCTAAGACCTACAG
CTACCTGACTCCCGACCTCTGGAAGGAGACTGTATTTACCAAGTCTCCCGATCAGGAATTCACTGATCACCTCATCAAGA
CCCACACCAGAGTCTCTGTGCAGCAGACCCAGGCTCCAGCTGTGGCTACAACA

Alignment

ORF - retro_ggor_390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGI--RGRG---RGGKAEDKEWMPVTKLGRLVKDMKIKSL
          M.DD..A.GGPGGPGGPGMGN.GGFRGGFGSGI..RGRG...RGGKAEDKEWMPVTKLG.LVKDMKIKS.
Retrocopy MVDDTSAVGGPGGPGGPGMGNCGGFRGGFGSGIRGRGRGRGARGGKAEDKEWMPVTKLGCLVKDMKIKSR

Parental  EEIYLFSL-PIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEV
          EEIYLFSL.P.....IIDFFLGASLKDEVLKIMPVQ.QTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEV
Retrocopy EEIYLFSL>PLR-NQIIDFFLGASLKDEVLKIMPVQTQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEV

Parental  ATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMA
          ATAI.GAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRC.S.LV.LIP.PRGTGIVSAPVPKKLLMMA
Retrocopy ATAIHGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCSSALVHLIPVPRGTGIVSAPVPKKLLMMA

Parental  GIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQA
          GI.DCYTSA.GCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSP.QEFTDHL.KTHTRVSVQ.TQA
Retrocopy GINDCYTSAWGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPDQEFTDHLIKTHTRVSVQQTQA

Parental  PAVATT
          PAVATT
Retrocopy PAVATT

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	43.93 RPM
SRP007412_cerebellum	0.16 RPM	30.06 RPM
SRP007412_heart	0.06 RPM	68.48 RPM
SRP007412_kidney	0.00 RPM	90.00 RPM
SRP007412_liver	0.03 RPM	206.12 RPM
SRP007412_testis	0.31 RPM	50.76 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_390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_390 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_385

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Felis catus	ENSFCAG00000029191	6 retrocopies	retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Gorilla gorilla	ENSGGOG00000009371	5 retrocopies	retro_ggor_129, retro_ggor_1391, retro_ggor_1428, retro_ggor_168, retro_ggor_390 ,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Microcebus murinus	ENSMICG00000012765	28 retrocopies	retro_mmur_1192, retro_mmur_1273, retro_mmur_1283, retro_mmur_1296, retro_mmur_1407, retro_mmur_1417, retro_mmur_1440, retro_mmur_153, retro_mmur_1613, retro_mmur_205, retro_mmur_210, retro_mmur_226, retro_mmur_230, retro_mmur_259, retro_mmur_266, retro_mmur_463, retro_mmur_672, retro_mmur_698, retro_mmur_742, retro_mmur_802, retro_mmur_824, retro_mmur_829, retro_mmur_875, retro_mmur_953, retro_mmur_966, retro_mmur_969, retro_mmur_981, retro_mmur_99,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tupaia belangeri	ENSTBEG00000006726	30 retrocopies	retro_tbel_1023, retro_tbel_1059, retro_tbel_1105, retro_tbel_1179, retro_tbel_129, retro_tbel_1444, retro_tbel_1545, retro_tbel_1615, retro_tbel_1622, retro_tbel_1786, retro_tbel_1910, retro_tbel_2294, retro_tbel_2749, retro_tbel_2786, retro_tbel_2973, retro_tbel_3179, retro_tbel_3314, retro_tbel_3509, retro_tbel_3523, retro_tbel_3682, retro_tbel_3701, retro_tbel_392, retro_tbel_4373, retro_tbel_463, retro_tbel_4674, retro_tbel_481, retro_tbel_586, retro_tbel_603, retro_tbel_639, retro_tbel_647,