RetrogeneDB ID: retro_ggor_1694

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:77460021..77461138(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSGGOG00000008224
• Aliases: None
• Description: None

Sequence

>retro_ggor_1694
GAGGGGACAGGGTCAGACTTAGGAATGGTGGCCTTCATGTTCTATAGCTGACAATTAGCTGCCACTTTTCACAGCCATCA
GTCCCAGACCATAGTACAGTCTACTGCCCAGGTTCTGGGAATTTCTGAGCTGTTTAATAACCAATAACTCCAAGTACAGC
AGCAACAGCAAAAGAATCTCTCACTACATGAATATATGAATATGAAATTGTTGCAAGAAGCTGGTGTCTCCCTTCCAAAG
GATATGTGGCAAAGTCACCAGATGAAGCTGACGCAATTGTCAAAAAATTAGGTTCTAAAGATGTTGTGATAATGGCACAG
AATTTTGCTTGTGGTAGACAAAAAGGAACATTTGAAAGCAGTCCCAAAAAAGGAGTGAAGATAGTTTTCTATCAAGAAGA
AAAAGCTGTTTCCTCTCGAATTATTGGGAAAAAGTTGTTTACCAAGTAAAAAGGAGAAAAGGACAAAATATGCAATCAAG
TATTGATCTGTGAGCAAAAATATCCCAGGAGAGAATACTACTTTCCAGTAACAATGGAAAGGTCATTTCAAGGTCCAGTA
TAAATAGGAAGTTTGCAAGGTGGTGTCAACACTGAAGATGTTTCTGCTGAGACTCCTGATGTAATAAAGAATCTATTGAT
GTCGTAGAAGGCATCAAAAAGGAACAAGCTCTCCAGCTTGCACAGAATATAAGCTTTCCATCTACTATTGTGGATTCTGT
GGCAGAAAACATGGTCAAGCTTTACAATCTTTTTCTGAACTACAACACAACCATGATAAAAATAAGCTCAATGGTATAAG
ATTCAGATGGAGCTCTGCTATGTTTGGACACAAAGATCAATTTTGATTCTAATTCAGTCTATCGCCAGAAGATCTTTGAT
CTACAGGACTGGACTCAGAAAGTGGAAAGGAACAAAGATGAAGCTAAGCCACATCTCAATAACACTGGCCTCAGTGGAAA
AATAGGCTGTCCAGTAAATGGTGCTGGTTTGGCTATAACCACAATAGATATAAGAAAACTTCATAAAGAGACTCCAACCA
GCTTCCTTGTTGTTTATGTTAGTGCTATAGTCCATCAAGTAACAGAATCACTTATGCTTATCACTTCAGATAAAAAG

Alignment

ORF - retro_ggor_1694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.71 %
• Parental protein coverage: 79.87 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGTGSDSEMAASMFYGRLVAVAILRSHRPRTAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSME
          EGTGSD..M.A.MFY....A.A...SH...T.....AQVLG.S.LFNN..LQVQQQQQ.NLSLHEYM.M.
Retrocopy EGTGSDLGMVAFMFYS*QLA-ATFHSHQSQTIVQSTAQVLGISELFNNQ*LQVQQQQQKNLSLHEYMNMK

Parental  LLQEAGVSVPK-GYVAKSPDEAYAIAKKLGSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAV
          LLQEAGVS.PK.GYVAKSPDEA.AI.KKLGSKDVVI.AQ..A.GR.KGTFES..K.GVKIVF..EE.KAV
Retrocopy LLQEAGVSLPK<GYVAKSPDEADAIVKKLGSKDVVIMAQNFACGRQKGTFESSPKKGVKIVFYQEE-KAV

Parental  SSQMIGKKLFTKQTGEKGRICNQVLVCERKYPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAETPE
          SS..IGKKLFTK..GEK..ICNQVL.CE.KYPRREYYF..TMERSFQGPV.IGS..GGVN.EDV.AETP.
Retrocopy SSRIIGKKLFTK*KGEKDKICNQVLICEQKYPRREYYFPVTMERSFQGPV*IGSLQGGVNTEDVSAETPD

Parental  AIIK-EPIDIEEGIKKEQALQLAQKMGFPPNIVESAAENMVKLYSLFLKYDATMIEINPMVEDSDGAVLC
          ..IK.E.ID..EGIKKEQALQLAQ...FP..IV.S.AENMVKLY.LFL.Y..TMI.I..MV.DSDGA.LC
Retrocopy -VIK<ESIDVVEGIKKEQALQLAQNISFPSTIVDSVAENMVKLYNLFLNYNTTMIKISSMV*DSDGALLC

Parental  MDAKINFDSNSAYRQKKIFDLQDWTQEDERDKDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGG
          .D.KINFDSNS.YRQ.KIFDLQDWTQ..ER.KD.AK..LN..GL.G.IGC.VNGAGLA..T.DI.KLH..
Retrocopy LDTKINFDSNSVYRQ-KIFDLQDWTQKVERNKDEAKPHLNNTGLSGKIGCPVNGAGLAITTIDIRKLHKE

Parental  TPANFLDVGGGATVHQVTEAFKLITSDKK
          TP..FL.V...A.VHQVTE...LITSDKK
Retrocopy TPTSFLVVYVSAIVHQVTESLMLITSDKK

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	66.85 RPM
SRP007412_cerebellum	0.00 RPM	36.21 RPM
SRP007412_heart	0.00 RPM	17.48 RPM
SRP007412_kidney	0.00 RPM	45.22 RPM
SRP007412_liver	0.00 RPM	11.47 RPM
SRP007412_testis	0.00 RPM	37.81 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_1694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1694 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2281
Pan troglodytes	retro_ptro_1615
Pongo abelii	retro_pabe_1939

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694 , retro_ggor_2327,
Gorilla gorilla	ENSGGOG00000027438	1 retrocopy	retro_ggor_825,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,