RetrogeneDB ID: retro_ggor_1428

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:12503639..12504485(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ggor_1428
ATGGCTGATGACGCAGGTGCGGCGCGGGGGTCCAGAGGCCCTGGGGACCCTGGGATGGGGAACCGCAGTGGCTTCCGCGG
AGATTTCGGCAGTGGCATCCGGGGCCGGGGCCGCGGAGCTCTGAGAGGCAAGGCCGAGGATAAGAAGTGGATGCCCGTTA
CCAAGCTGGGCTGCCTGGTCAAGGACATGAAGATCTAGTCCCTGGAGGAGATCTATCTCTTCTCCCTGCCCATCAAGGAA
TCTGAGATCATTGACTTGTTCCTGGGGGCCTCTCTCAAGGATGAAGTTTTGATTACACCAGTGCAGAAGCAGACCCGTGC
CGGCCAGCGCACCAGGTTCAAGGCGTTTGTTGCCATTGGGGACTACAATGGCCATGTCTGTCTGGGAGTTAAGTGCTCCA
AGGAGGCAGCCACTGCCATCCGCGGGGCCATCATCCTGGCCAAGCTCTCCACTGTCCTCGTGCACAGAGGCTACTGGGGG
AACAAGATCGGCAAGCCCCACACCGTCCCTTGCAAGGTGACAGGCCACTGCGGCTCTGTGCTGGTGCGCCTCATCCCCGC
ACCCAGGGACACTGGCATCGTCTCAGCGCCTGTGCCCAAGAAGCTGCTCATGATGGCTGGTATCGGTGACTGATACACCT
CAGCCCGGGGCTGCACTGCCACCCTGGGCAACTTCACCAAGGCCACCTTTGATGTCATCTCTAAGACCTACAGCTACCTA
ACCCCTGACCTCTGAAAGGAGACTGTATTCACCAAGTCTCCCTATGAGGAATTCACTGACCACCTCGTTAAGACCGACAC
CAGAGTCTCTGTGCAGAGGACCCAGGCTCCAGCTGTGGCTACAACA

Alignment

ORF - retro_ggor_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRG---GKAEDKEWMPVTKLGRLVKDMKIKSLEE
          MADDAGAA.G..GPG.PGMGNR.GFRG.FGSGIRGRGRG...GKAEDK.WMPVTKLG.LVKDMKI.SLEE
Retrocopy MADDAGAARGSRGPGDPGMGNRSGFRGDFGSGIRGRGRGALRGKAEDKKWMPVTKLGCLVKDMKI*SLEE

Parental  IYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATA
          IYLFSLPIKESEIID.FLGASLKDEVL.I.PVQKQTRAGQRTRFKAFVAIGDYNGHV.LGVKCSKE.ATA
Retrocopy IYLFSLPIKESEIIDLFLGASLKDEVL-ITPVQKQTRAGQRTRFKAFVAIGDYNGHVCLGVKCSKEAATA

Parental  IRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGID
          IRGAIILAKLS.V.V.RGYWGNKIGKPHTVPCKVTG.CGSVLVRLIPAPR.TGIVSAPVPKKLLMMAGI.
Retrocopy IRGAIILAKLSTVLVHRGYWGNKIGKPHTVPCKVTGHCGSVLVRLIPAPRDTGIVSAPVPKKLLMMAGIG

Parental  DCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAV
          D.YTSARGCTATLGNF.KATFD.ISKTYSYLTPDL.KETVFTKSPY.EFTDHLVKT.TRVSVQRTQAPAV
Retrocopy D*YTSARGCTATLGNFTKATFDVISKTYSYLTPDL*KETVFTKSPYEEFTDHLVKTDTRVSVQRTQAPAV

Parental  ATT
          ATT
Retrocopy ATT

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	0.10 RPM	43.93 RPM
SRP007412_cerebellum	0.28 RPM	30.06 RPM
SRP007412_heart	0.22 RPM	68.48 RPM
SRP007412_kidney	0.20 RPM	90.00 RPM
SRP007412_liver	0.21 RPM	206.12 RPM
SRP007412_testis	0.10 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_1428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1428 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1965

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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,