RetrogeneDB ID: retro_ptro_526

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:125244906..125245782(-)
• Located in intron of: ENSPTRG00000003037

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDOA
• Ensembl ID: ENSPTRG00000007983
• Aliases: None
• Description: Pan troglodytes aldolase A, fructose-bisphosphate (ALDOA), mRNA. [Source:RefSeq mRNA;Acc:NM_001144833]

Sequence

>retro_ptro_526
ATGCCCTACCAATATCCAGCATTGACCCTGGAGCAGAAGAAGGAGCTGTCTGACATCGCTCACCGCATCGTGGCCCTGGG
CAAGGGCATCCTGGCTGCAGATGAGTCCAATGGGAGCATTGCCAAGTGGCTGCAGTCCCTTGGCGCCGAGAACACCAAAG
AGAACCGGCGCTTCTACCGTCAGCTGCTGCTGACAGCTGACGACTGAGTGAACCCCTGCATCGGGGACGTCATCCTCTTC
CACCAGACACTCTACCAGAGAAGGATGATGGGCGTCCTTTCCCCCAAGTTGTCATATCCAAGGGTGGTGTTGGGGGCAGC
AAGGTAGACAAGGGCGTGGTCCCCCTTGCAGGGACAAATGGCAAGACCACCACCCAAGGGTTGTATGGGCTGTCTGAGTG
CTGTGCCCAGTACAAGAAGGATGGAGCTGACTTCACCAAGTGGCATTGTGTTCTGAAGATTGAGGAACACACCCCCTCAG
CCCTTGCCGTCATGGAAAATACCAACGTCCTGGCCTGTTATGCCAGCATCTGCTAGCAGAGTGGCATTGTGCCCATTGCG
GAGCCTGAGATCCTCCCTAATGGGGACCATGACTTGAAGCACTGCCAGTGTGTGACCAAGAAGGTGCTGACTGCTGTCTA
CAAGGCTCTGAGTGATCAACACATCTATCTTGGAAGGCATCTTGCTGAACCCCAGCATGGTCACCCCAGGCCATCCCTGC
ATCCAGAAGTTTTCTCACGAGGAGATTGCCATGGTGACTGTCACAACGCTGCACCGCACAGTGCCCCCCGCTGTTCCTGG
GATCACATTCCTGTCTGGAGGCCAGAATGAGGAGGAGGCATCCATCAACCTCAACGCCATTAACAAGTGCTCCCTG

Alignment

ORF - retro_ptro_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.01 %
• Parental protein coverage: 80.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPYQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRV
          MPYQYPALT.EQKKELSDIAHRIVA.GKGILAADES.GSIAK.LQS.G.ENT.ENRRFYRQLLLTADD.V
Retrocopy MPYQYPALTLEQKKELSDIAHRIVALGKGILAADESNGSIAKWLQSLGAENTKENRRFYRQLLLTADD*V

Parental  NPCIGGVILFHETLYQKA-DDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYK
          NPCIG.VILFH.TLYQ...DDGRPFPQV..SKGGV.G.KVDKGVVPLAGTNG.TTTQGL.GLSE.CAQYK
Retrocopy NPCIGDVILFHQTLYQRR<DDGRPFPQVVISKGGVGGSKVDKGVVPLAGTNGKTTTQGLYGLSECCAQYK

Parental  KDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKV
          KDGADF.KW.CVLKI.EHTPSALA.MEN.NVLA.YASIC.Q.GIVPI.EPEILP.GDHDLK.CQ.VT.KV
Retrocopy KDGADFTKWHCVLKIEEHTPSALAVMENTNVLACYASIC*QSGIVPIAEPEILPNGDHDLKHCQCVTKKV

Parental  LAAVYKALSDHHIY-LEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSEE
          L.AVYKALSD.HIY.LEG.LL.P.MVTPGH.C.QKFSHEEIAM.TVT.L.RTVPPAV.GITFLSGGQ.EE
Retrocopy LTAVYKALSDQHIY>LEGILLNPSMVTPGHPCIQKFSHEEIAMVTVTTLHRTVPPAVPGITFLSGGQNEE

Parental  EASINLNAINKCPL
          EASINLNAINKC.L
Retrocopy EASINLNAINKCSL

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	1253.86 RPM
SRP007412_cerebellum	0.00 RPM	694.78 RPM
SRP007412_heart	0.00 RPM	881.61 RPM
SRP007412_kidney	0.00 RPM	649.92 RPM
SRP007412_liver	0.00 RPM	195.55 RPM
SRP007412_testis	0.00 RPM	92.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_526 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_526 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_740
Gorilla gorilla	retro_ggor_621
Pongo abelii	retro_pabe_636

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526 ,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,