RetrogeneDB ID: retro_ptro_1615

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:77109572..77110605(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSPTRG00000005859
• Aliases: None
• Description: None

Sequence

>retro_ptro_1615
CAGACCATAGTACAGTCTACTGCCCAGGTTCTGGGAATTTCTGAGCTGTTTAATAACCAATAACTCCAAGTACAGCAGCA
ACAGCAAAAGAATCTCTCACTACATGAATCTATGAATATGAAATTGTTGCAAGAAGCTGGTGTCTCCCTTCCAAAGGATA
TGTGGCAAAGTCACCAGATGAAGCTGACGCAATTGTCAAAAAATTAGGTTCTAAAGATGTTGTGATAATGGCACAGAATT
TTGCTTGTGGTAGACAAAAAGGAACATTTGGAAGCAGTCCCAAAAGAGGAGTGAAGATAGTTTTCTATCAAGAAGAAAAA
GCTGTTTCCTCTCAAATTATTGGGAAAAAGTTGTTTACCAAGTAAACAGGAGAAAAGGACAAAATATGCAATCAAGTATT
GATCTGTGAGCAAAAATATCCCAGGAGAGAATACTACTTTCCAGTAAAAATGGAAAGGCCATTTCAAGGTCCAGTATAAA
TAGGAAGTTTGCAAGGTGGTGTCAACACTGAAGATGTTTCTGCTGAGACTCCTGATGTAATAAAGAATCTATTGATGTCG
TAGAAGGCATCAAAAAGGAACAAGCTCTCCAGCTTGCACAGAATATAAGATTTCCATCTACTATTGTGGATTCTGTGGCA
GAAAACATGGTCAAGCTTTACAATCTTTTTCTGAACTACAACACAACCATGATAAAAAATAAGCTCAATGGTATAAGATT
CAGATGGAGCTCTGCTATGTTTGGACACAAAGATCAATTTTGATTCTAATTCAGTCTATCGCCAGAAGATCTTTGATCTA
CAGGACTGGACTTAGGAAGATGAAAGGAACAAAGATGAAGCTAAGCCACATCTCAATAACACTGGCCTCAGTGGAAAAAT
AGGCTGTCTAGTAAATGGTGCTGGTTTGGCTCTGACCACAATAGATATAAGAAAACTTCATAAAGAGACTCCACCAGCTT
CCTTGTTGTTCATGTTAGTGTTATACTCCATCAAGTAACAGAATCACTTATGCTTATCACTTCAGATAAAAAG

Alignment

ORF - retro_ptro_1615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.31 %
• Parental protein coverage: 75.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RTAQRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMELLQEAGVSVPK-GYVAKSPDEAYAIAKKL
          .T.....AQVLG.S.LFNN..LQVQQQQQ.NLSLHE.M.M.LLQEAGVS.PK.GYVAKSPDEA.AI.KKL
Retrocopy QTIVQSTAQVLGISELFNNQ*LQVQQQQQKNLSLHESMNMKLLQEAGVSLPK<GYVAKSPDEADAIVKKL

Parental  GSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCER
          GSKDVVI.AQ..A.GR.KGTF.S..K.GVKIVF..EE.KAVSSQ.IGKKLFTK.TGEK..ICNQVL.CE.
Retrocopy GSKDVVIMAQNFACGRQKGTFGSSPKRGVKIVFYQEE-KAVSSQIIGKKLFTK*TGEKDKICNQVLICEQ

Parental  KYPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIK-EPIDIEEGIKKEQALQLAQKMGFP
          KYPRREYYF...MER.FQGPV.IGS..GGVN.EDV.AETP...IK.E.ID..EGIKKEQALQLAQ...FP
Retrocopy KYPRREYYFPVKMERPFQGPV*IGSLQGGVNTEDVSAETPD-VIK<ESIDVVEGIKKEQALQLAQNIRFP

Parental  PNIVESAAENMVKLYSLFLKYDATMI-EINPMVEDSDGAVLCMDAKINFDSNSAYRQKKIFDLQDWTQED
          ..IV.S.AENMVKLY.LFL.Y..TMI..I..MV.DSDGA.LC.D.KINFDSNS.YRQ.KIFDLQDWT.ED
Retrocopy STIVDSVAENMVKLYNLFLNYNTTMI>KISSMV*DSDGALLCLDTKINFDSNSVYRQ-KIFDLQDWT*ED

Parental  ERDKDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTP-ANFLDVGGGATVHQVTEAFKLITSD
          ER.KD.AK..LN..GL.G.IGCLVNGAGLA..T.DI.KLH..TP...FL.V......HQVTE...LITSD
Retrocopy ERNKDEAKPHLNNTGLSGKIGCLVNGAGLALTTIDIRKLHKETP<TSFLVVHVSVILHQVTESLMLITSD

Parental  KK
          KK
Retrocopy KK

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	0.02 RPM	52.16 RPM
SRP007412_cerebellum	0.00 RPM	40.80 RPM
SRP007412_heart	0.03 RPM	90.79 RPM
SRP007412_kidney	0.00 RPM	56.54 RPM
SRP007412_liver	0.00 RPM	8.67 RPM
SRP007412_testis	0.00 RPM	19.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1615 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1615 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2281
Gorilla gorilla	retro_ggor_1694
Pongo abelii	retro_pabe_1939

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 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,
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,