RetrogeneDB ID: retro_ggor_2428

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:59692615..59693440(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP4
• Ensembl ID: ENSGGOG00000011313
• Aliases: None
• Description: None

Sequence

>retro_ggor_2428
ATGGCCGACAAGGAAGCAGCCTTTGACGACGCAGTGGAAGAATGAGTGATCAACAAGGAGTACAAAAAATGGAAAAAGAA
CACCCCTTTTCTTTATGATTTGGTGTTGACCCATGCTCTGGAGTGGCCCAGCCTAACTGCCCAGTGGCTTCCAGATGTAA
CCAGACCAGAAGGGAAAGATTTCAGCATTCATCAACTTGTCCTGGGGACATACACATTGGATGAACAAAACCATCTCGTT
ATAGCCAGTGTGCAACTCCCTAATGACACTCAGTTTGATGCGTCACACTACAACACTGAGAAAGGAGAATTTGGAGGTTT
TTATTCAGTTAGAGGAAAAATTGAAATAGAAATCAAGATCAACCATGAAGGAGAAGTGAACAAGGTCCGTTATATGCCCC
AGAACCCTTGTATCATCTCAACTAATACTCCTTCCAGTGATGTTCTTGTCTTTGACTATACAAAACACCCTTCTAAACCA
GATCCTTCTGGAGAGTGCGATCCAGACTTGTGTCTCCGTGGACATCAGAAGGAAGGCTATGGGCTTTCTTGGAACCCAAA
TCTCTGTGGGCACTTACTTAGTGCTTCAGATGACCACACCAGCAGCCTGTGGGACAGCAGTGCTGTCCCAAAGGAGGGAA
AAGTGGTGGATGTGAAGACCATCTTTACAGGGCATACAGCAGTAGTAGAAGATGTTTCCTGGCATCTGCTCCATGAGTCT
CTGTTTGGGTCAGTTGCTGATGATCAGAAACTTATGATTTGGGATATTTGTTCAAACAGTGCTTCCAAACCAAGCCATTC
AGTTGACGCTCACACTGCTGAAGTG

Alignment

ORF - retro_ggor_2428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.17 %
• Parental protein coverage: 64.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTSYRPEGKDFSIHRLVL
          MADKEAAFDDAVEE.VIN.EYK.WKKNTPFLYDLV.THALEWPSLTAQWLPDVT..RPEGKDFSIH.LVL
Retrocopy MADKEAAFDDAVEE*VINKEYKKWKKNTPFLYDLVLTHALEWPSLTAQWLPDVT--RPEGKDFSIHQLVL

Parental  GTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPC
          GT.T.DEQNHLVIASVQLPND..QFDASHY..EKGEFGGF.SV.GKIEIEIKINHEGEVN..RYMPQNPC
Retrocopy GTYTLDEQNHLVIASVQLPND-TQFDASHYNTEKGEFGGFYSVRGKIEIEIKINHEGEVNKVRYMPQNPC

Parental  IIATKTPSSDVLVLDYTKHP-KPDLSGDCNSDLHLHGHQKKGYGLSW-PNLSGHLLSASDDHTIYPWDIS
          II.T.TPSSDVLV.DYTKHP.KPD.SG.C..DL.L.GHQK.GYGLSW.PNL.GHLLSASDDHT...WD.S
Retrocopy IISTNTPSSDVLVFDYTKHPSKPDPSGECDPDLCLRGHQKEGYGLSWNPNLCGHLLSASDDHTSSLWDSS

Parental  AVPKEGNVVDAKTIFTGHTVVVEDVSWHLFHESLFGSVADHQKLRIWDTCSNNTSKPSHSVEAHTAEV
          AVPKEG.VVD.KTIFTGHT.VVEDVSWHL.HESLFGSVAD.QKL.IWD.CSN..SKPSHSV.AHTAEV
Retrocopy AVPKEGKVVDVKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDICSNSASKPSHSVDAHTAEV

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	1.68 RPM	33.86 RPM
SRP007412_cerebellum	1.02 RPM	32.70 RPM
SRP007412_heart	0.34 RPM	7.54 RPM
SRP007412_kidney	1.27 RPM	47.84 RPM
SRP007412_liver	0.95 RPM	30.97 RPM
SRP007412_testis	6.84 RPM	172.29 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_2428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001021	7 retrocopies	retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus	ENSCPOG00000015352	3 retrocopies	retro_cpor_154, retro_cpor_27, retro_cpor_899,
Gorilla gorilla	ENSGGOG00000011313	4 retrocopies	retro_ggor_1022, retro_ggor_1314, retro_ggor_1867, retro_ggor_2428 ,
Gorilla gorilla	ENSGGOG00000013437	1 retrocopy	retro_ggor_1366,
Macaca mulatta	ENSMMUG00000009940	1 retrocopy	retro_mmul_75,
Mustela putorius furo	ENSMPUG00000015214	1 retrocopy	retro_mputfur_104,
Otolemur garnettii	ENSOGAG00000011632	2 retrocopies	retro_ogar_3079, retro_ogar_3297,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Rattus norvegicus	ENSRNOG00000021492	1 retrocopy	retro_rnor_1270,
Sarcophilus harrisii	ENSSHAG00000010923	1 retrocopy	retro_shar_399,
Tupaia belangeri	ENSTBEG00000002236	3 retrocopies	retro_tbel_1360, retro_tbel_1718, retro_tbel_3802,
Vicugna pacos	ENSVPAG00000011876	4 retrocopies	retro_vpac_333, retro_vpac_419, retro_vpac_652, retro_vpac_94,