RetrogeneDB ID: retro_ggor_2904

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:48635131..48635974(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WASF2
• Ensembl ID: ENSGGOG00000004436
• Aliases: None
• Description: None

Sequence

>retro_ggor_2904
TTAGTAACGAGGAACATCGAGCCAAGGCACCTGTGCCGTCAGACGTTGCCTAGCGTTAGAAGCGAGCTGGAATGCGTGAC
CAACATCACCCTGGCAAATGTCATCCGACAGCTGGGCAGCCTGAGTAAATATGCAGAGGACATTTTTGGAGAGCTCTTTA
CTCAGGCAAATACCTTTGCCTCTCGGGTAAGCTCCCTTGCTGAGAGGGTCGACGGACTACAAGTTAAAGTCACTCAGCTG
GATCCCAAGGAAGAAGAAGTGTCACTGCAAGGAATCAACACCTGAAAAGCCTTCAGAAGCTCCACCATTCAAGACCAGAA
GCTTTTTGACAGAAACTCTCTCCCAGTGCCTGTCTTAGAAACATACAATACCTGTGATACTCCTCCCCCTCTCAACAATC
TTACCCCTTACAGGGACGATGGAACAGAGGCACTCAAATTCTACACAGACCCTTCATACTTCTTTGATCTTTGGAAGAAG
ATGCTGCAGGACACCAAGGATATCATGAAAGAGAAGAGAAAGCACAGGAAAGAAAAGAAAGATAATCCAAATCGAGGGAA
TGTAAACCCACGTAAAATCAAGACACATAAGGAAGAGTGGGAGAAAATTAAGATGGGGCAAGAATTTGTGGAGTCCAAAG
AAAAGCTGGGGCCTTCTGGGTATCCACCCACCTTGGTGTACCAGAATGGCAGCATTGGCTGTGTTGAAAACGTGGATGCA
AGTAGCTATCCACCACCATCACAGTCAGACTCTGCTTCTTCACCTTCTCCTCCCTTCTCCGAGGACAACTTGCCTCCTCC
ACCAGCAGAATTCAGTTACCCCGTGGACAACCAAAGAGGATCT

Alignment

ORF - retro_ggor_2904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.45 %
• Parental protein coverage: 57.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVTRNIEPRHLCRQTLPSVRSELECVTNITLANVIRQLGSLRSEYTSQLFLSPLPHCGIMQERMNCLKFR
          LVTRNIEPRHLCRQTLPSVRSELECVTNITLANVIRQLGSL.S.Y....F............R...L..R
Retrocopy LVTRNIEPRHLCRQTLPSVRSELECVTNITLANVIRQLGSL-SKYAEDIFGELFTQANTFASRVSSLAER

Parental  VXKKKKKKAQMSFKMEKVSLQGINTRKAFRSSTIQDQKLFDRNSLPVPVLETYNTCDTPPPLNNLTPYRD
          V.....K..Q...K.E.VSLQGINT.KAFRSSTIQDQKLFDRNSLPVPVLETYNTCDTPPPLNNLTPYRD
Retrocopy VDGLQVKVTQLDPKEEEVSLQGINT*KAFRSSTIQDQKLFDRNSLPVPVLETYNTCDTPPPLNNLTPYRD

Parental  DGKEALKFYTDPSYFFDLWKEKMLQDTKDIMKEKRKHRKEKKDNPNRGNVNPRKIKTRKEEWEKMKMGQE
          DG.EALKFYTDPSYFFDLWK.KMLQDTKDIMKEKRKHRKEKKDNPNRGNVNPRKIKT.KEEWEK.KMGQE
Retrocopy DGTEALKFYTDPSYFFDLWK-KMLQDTKDIMKEKRKHRKEKKDNPNRGNVNPRKIKTHKEEWEKIKMGQE

Parental  FVESKEKLGTSGYPPTLVYQNGSIGCVENVDASSYPPPPQSDSASSPSPSFSEDNLPPPPAEFSYPADNQ
          FVESKEKLG.SGYPPTLVYQNGSIGCVENVDASSYPPP.QSDSASSPSP.FSEDNLPPPPAEFSYP.DNQ
Retrocopy FVESKEKLGPSGYPPTLVYQNGSIGCVENVDASSYPPPSQSDSASSPSPPFSEDNLPPPPAEFSYPVDNQ

Parental  RGS
          RGS
Retrocopy RGS

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	1.73 RPM	31.65 RPM
SRP007412_cerebellum	1.18 RPM	25.92 RPM
SRP007412_heart	0.97 RPM	19.95 RPM
SRP007412_kidney	3.07 RPM	45.84 RPM
SRP007412_liver	0.92 RPM	18.41 RPM
SRP007412_testis	9.22 RPM	103.39 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_2904 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2904 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4682
Pongo abelii	retro_pabe_125

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000158195	1 retrocopy	retro_hsap_4682,
Gorilla gorilla	ENSGGOG00000004436	1 retrocopy	retro_ggor_2904 ,
Gorilla gorilla	ENSGGOG00000012518	1 retrocopy	retro_ggor_2411,
Nomascus leucogenys	ENSNLEG00000009635	1 retrocopy	retro_nleu_2175,
Pongo abelii	ENSPPYG00000001661	1 retrocopy	retro_pabe_125,