RetrogeneDB ID: retro_ggor_1829

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:19129857..19130973(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSGGOG00000002511
• Aliases: None
• Description: None

Sequence

>retro_ggor_1829
ATGCAGGTCACCCTGAAGACCCTCCAGCCGCAGACCTTGACCTTCAAGATAGACATTGACCCCGAGGAGACAGTGAAAGC
ACTGAAAGAGAAGACGGAATCTGAAAAGGGGAAAGATGCCTCTCTGGTAGCAGGTCAAACATTAATTTATGCAGGCAAAA
TCCTCAGTGATGATACTGCTCTCAAAGAATATAAAATTGATGAGTAAAACTTTGTGGTGGTTATGGTGACCAAACCCAAA
GCAGTGTCCACACCAGCACTAGCTACAACTCAGCAGTCAGCTCCTGCCAGCACTACAGCAGTTACTTCCTCCACAACAAC
AACTGTGGCTCAGGCTCCAACCCCTGTCCCTGCTTTGTCTCCCACTTTCACACCTGCATTCATCACTCCAGTATCAGTGA
CAGTGTCCTCTGAACCTGCAACTGCTAGTGCAACTAAACAAGAGAAACCTGCAGAAAAGCCAGCAGAGACACCAGTGGCT
ACTAGCCTGACATCAACTCATAGTACATCAGGAGATTCTTCTTGGTCAAACCTTTTTGAAGATGCAACGAGTGCACTTGT
GATGGGTCAGTCTTACGAGAATATGGTAACTGAGATCATGTCAATGGGCTAGGAACGAGAGCAAGTAATTGCAGCCCCAA
GAGCCAGTTCCAACAACCCTGACAGGGCAGTGGAGTACCTTTTAATGGGAATCCCTGGAGATAAAGTCAGGTTGTGGCTG
ACCCCCACCAAGCAGCTAGTACTGGGGCTCCTCAGTCTTCAACAGTGGCTGCAGCTGCAGCAACCACGACAGCAACAACT
ACAGCAAGTTCTGGAACATCCCCTTGAATTTTTATGGAATCAGTCTCAGTTTCAACAGATGAGACAAATTATTCAACAGA
GTCCTTCCCTTCTTCCAGTGTTACTACAGTAGATAGATCGAGAGAATCCTCAATTACTTCAGCAAATTAGCCAACACCAG
GAGCATTTTATTCAGATGTTAAATGAATCAGTTTGAGAAGCTGATGGTCAAAGAGGAAGAGGTGGAGGTGTCAGTGGAGG
AACTGCAGAAGCTGGAAATGGTCTCATGAACTACATTCAAGTAACGCCTCAGGAAAAAGAAGCTATAGAAAGGGTG

Alignment

ORF - retro_ggor_1829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.66 %
• Parental protein coverage: 91.2 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQVTLKTLQQQT--FKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKN
          MQVTLKTLQ.QT..FKIDIDPEETVKALKEK.ESEKGKDA..VAGQ.LIYAGKIL.DDTALKEYKIDE.N
Retrocopy MQVTLKTLQPQTLTFKIDIDPEETVKALKEKTESEKGKDASLVAGQTLIYAGKILSDDTALKEYKIDE*N

Parental  FVVVMVTKPKAVSTPAPATTQQSAPASTTAVTSSTTTTVAQAPTPVPALAPTSTPASITPASATASSEPA
          FVVVMVTKPKAVSTPA.ATTQQSAPASTTAVTSSTTTTVAQAPTPVPAL.PT.TPA.ITP.S.T.SSEPA
Retrocopy FVVVMVTKPKAVSTPALATTQQSAPASTTAVTSSTTTTVAQAPTPVPALSPTFTPAFITPVSVTVSSEPA

Parental  PASAAKQEKPAEKPAETPVATSPTATDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVI
          .ASA.KQEKPAEKPAETPVATS.T.T.STSGDSS.SNLFEDATSALV.GQSYENMVTEIMSMG.EREQVI
Retrocopy TASATKQEKPAEKPAETPVATSLTSTHSTSGDSSWSNLFEDATSALVMGQSYENMVTEIMSMG*EREQVI

Parental  AALRASFNNPDRAVEYLLM-GIPGDRESQAVVDPPQAASTGAPQSSAVAAAAATTTATTTTTSSGGHP-L
          AA.RAS.NNPDRAVEYLLM.G.P..R.SQ.V.DP.QAASTGAPQSS.VAAAAATTTATTT..SSG..P.L
Retrocopy AAPRASSNNPDRAVEYLLM<GNPW-R*SQVVADPHQAASTGAPQSSTVAAAAATTTATTT-ASSGTSP<L

Parental  EF-LRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGG
          .F.L.NQ.QFQQMRQIIQQ.PSLLP.LLQ.I.RENPQLLQQISQHQEHFIQMLNE.V.EA.GQ.G.GGG.
Retrocopy NF<LWNQSQFQQMRQIIQQSPSLLPVLLQ*IDRENPQLLQQISQHQEHFIQMLNESV*EADGQRGRGGGV

Parental  SGGIAEAGSGHMNYIQVTPQEKEAIERL
          SGG.AEAG.G.MNYIQVTPQEKEAIER.
Retrocopy SGGTAEAGNGLMNYIQVTPQEKEAIERV

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	0.77 RPM	87.47 RPM
SRP007412_cerebellum	0.24 RPM	68.71 RPM
SRP007412_heart	0.06 RPM	19.29 RPM
SRP007412_kidney	0.41 RPM	69.39 RPM
SRP007412_liver	0.21 RPM	87.23 RPM
SRP007412_testis	0.10 RPM	160.68 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_1829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1829 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1760

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829 ,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,