RetrogeneDB ID: retro_pabe_636

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:125305829..125306706(-)
• Located in intron of: ENSPPYG00000002747

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDOA
• Ensembl ID: ENSPPYG00000007244
• Aliases: None
• Description: fructose-bisphosphate aldolase A [Source:RefSeq peptide;Acc:NP_001127068]

Sequence

>retro_pabe_636
ATGCCGTACCAATATCCAGCATTGACCCTGGAGCAGAAGAAGGAGCTGTCTGACATCGCTCACCGCATCATGGCACTGGG
TGAGGGCATCCTGACTGCAGATGAGTCCACTGGGAGCATTGCCAAGCAGCCGCAGTCCCTTGGCGCTGAGAACACCGAAG
AGAACCGGCGCTTCTACCATCAGCTGCTGCTGACAGCTGACGACTGCGTGAACCCCTGCATCGGGCACGTCATCCTCTTC
CACCAGACACTCTACCAGAAGAAGGATGATGGGCGTCCTTTCCCCCAAGTTATCATATCCAAGGGTGGTGTTGGGGGCAT
CAAGGTAGACAAGGGCGTGGTCCCCCTTGCAGGGACAAATGGCGAGACCACCACCCAAGGGTTGTATGGGCTGTCTGAGT
GCTGTGCCCAGTACAAGAAGGATGGAGCTGACTTCACCAAGTGGCATTGTGTTCTGAAGATTGGGGAACACACCCCCTCA
GCCCTTGCCATCATGGAAAATACCAACGTCCTGGCCTGTTATGCCAGCATCTGCTAGCAGAATGGCATTGTGCCCATTGC
GGAGCCTGAGATCCTCCCTAATGGGGACCATGACTTGAAGCGCTGCCACTGTGTGACCAAGAAGGTGCTGATTGCTGTCT
ATGAGGCTCTGAGTGATCAACACATCTATCTTGGAAGGCATCTTGCTGAACCCCAACATGGTCACCCCAGGCCATCCCTG
CATCCAGAATTTTTCTCACGAGGAGATTGCCATGGCAACTATCACAACGCTGCGCCGCACAGTGCCCCCCGCTGTCCCTG
GGATCACCTTCCTGTCTGGAGGCCAGAATGAGGAGGAGGCATCCATCAACTTCAAAGCCATTAACAAGTGCCCCCTG

Alignment

ORF - retro_pabe_636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.98 %
• Parental protein coverage: 80.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPYQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADNRV
          MPYQYPALT.EQKKELSDIAHRI.A.G.GIL.ADESTGSIAK..QS.G.ENTEENRRFY.QLLLTAD..V
Retrocopy MPYQYPALTLEQKKELSDIAHRIMALGEGILTADESTGSIAKQPQSLGAENTEENRRFYHQLLLTADDCV

Parental  NPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKK
          NPCIG.VILFH.TLYQK.DDGRPFPQVI.SKGGV.GIKVDKGVVPLAGTNGETTTQGL.GLSE.CAQYKK
Retrocopy NPCIGHVILFHQTLYQKKDDGRPFPQVIISKGGVGGIKVDKGVVPLAGTNGETTTQGLYGLSECCAQYKK

Parental  DGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVL
          DGADF.KW.CVLKIGEHTPSALAIMEN.NVLA.YASIC.QNGIVPI.EPEILP.GDHDLKRC..VT.KVL
Retrocopy DGADFTKWHCVLKIGEHTPSALAIMENTNVLACYASIC*QNGIVPIAEPEILPNGDHDLKRCHCVTKKVL

Parental  AAVYKALSDHHIY-LEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSEEE
          .AVY.ALSD.HIY.LEG.LL.PNMVTPGH.C.Q.FSHEEIAMAT.T.LRRTVPPAV.GITFLSGGQ.EEE
Retrocopy IAVYEALSDQHIY>LEGILLNPNMVTPGHPCIQNFSHEEIAMATITTLRRTVPPAVPGITFLSGGQNEEE

Parental  ASINLNAINKCPL
          ASIN..AINKCPL
Retrocopy ASINFKAINKCPL

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	0.06 RPM	1093.21 RPM
SRP007412_cerebellum	0.00 RPM	421.47 RPM
SRP007412_heart	0.09 RPM	661.40 RPM
SRP007412_kidney	0.03 RPM	579.84 RPM
SRP007412_liver	0.00 RPM	201.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_636 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_636 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_740
Pan troglodytes	retro_ptro_526
Gorilla gorilla	retro_ggor_621

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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,