RetrogeneDB ID: retro_ptro_1580

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:24185076..24185787(-)
• Located in intron of: ENSPTRG00000011702

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM1
• Ensembl ID: ENSPTRG00000002807
• Aliases: None
• Description: Pan troglodytes phosphoglycerate mutase 1 (brain) (PGAM1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246485]

Sequence

>retro_ptro_1580
ATGGCCACCTACAAACTGGTGCTGATCTGGCCCAGTGAGAGCACCTGGAACCTGGAGAACTGCTTCAGCGACTGGTACAA
TGCCAACGTGAGCCCGGCGGGCCATAAGGAGATGAAGAGTGGCAGGCAGGCAGGCACTGTGAGATGGCTGGCTATGAGTT
TGACATCTGCTTCACCTCAGTGCAGAAGAGAGCAATCTGGACCCTCTGGACAGTGCTAGATGCCATTGATCAGATGTGGT
TGCCTGTAGTGAGGACTTGGTGCCTCAGTGAGCAGCACTATGGGGGTCTGACTGATCTCAGTAAAGCAGAAACTGCTGCA
AAGCATGATGAGGCCCAGGTGAAGATCTGGAGGCTCTCCTATGATGTTCCACCACCTCCGATGGAGCCTGACCATCCTTT
CTACAGCAACATTAGTAAGGATCGCAGGCATGCAGACCTCACGGAGGATCAGCTACCCTCCTGTGAGAGTCTGAAGGACT
CTCAAAGCCAGAGCTCTGCCGTTTTGGAATGAAGAAATAGCTCACCTGGTAAAAGAGGGGAAATGGGTGCTGATTGCAGT
GCATGGCAACAGCCTCTGGGGCATTGTGAAACATTTGGAGGGTCTCTCTGAAGAGGCTGTCATGGAGCTGAACCTGCCGA
CTAGTATTCCCATTGTCTATGAATTCGACAAGAACTTGAAGACCATCAGGTGCATGCAGTTCCTGGGGGAT

Alignment

ORF - retro_ptro_1580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.64 %
• Parental protein coverage: 92.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAYKLVLIRHGESAWNLENRFSGWYDADLS-PAGH--EEAKRGGQALRDAGYEFDICFTSVQKRAIRTL
          MA.YKLVLI...ES.WNLEN.FS.WY.A..S.P.G....E....G.....AGYEFDICFTSVQKRAI.TL
Retrocopy MATYKLVLIWPSESTWNLENCFSDWYNANVS<PGGP*GDEEWQAGRHCEMAGYEFDICFTSVQKRAIWTL

Parental  WTVLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNIS
          WTVLDAIDQMWLPVVRTW.L.E.HYGGLT.L.KAETAAKH.EAQVKIWR.SYDVPPPPMEPDHPFYSNIS
Retrocopy WTVLDAIDQMWLPVVRTWCLSEQHYGGLTDLSKAETAAKHDEAQVKIWRLSYDVPPPPMEPDHPFYSNIS

Parental  KDRRYADLTEDQLPSCESLKDT-IARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIM
          KDRR.ADLTEDQLPSCESLKD...ARALPFWNEEI....KEGK.VLIA.HGNSL.GIVKHLEGLSEEA.M
Retrocopy KDRRHADLTEDQLPSCESLKDS>KARALPFWNEEIAHLVKEGKWVLIAVHGNSLWGIVKHLEGLSEEAVM

Parental  ELNLPTGIPIVYELDKNLKPIKPMQFLGD
          ELNLPT..................QFLGD
Retrocopy ELNLPTXXXXXXXXXXXXXXXXXXQFLGD

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	0.11 RPM	300.77 RPM
SRP007412_cerebellum	0.14 RPM	131.31 RPM
SRP007412_heart	0.03 RPM	48.94 RPM
SRP007412_kidney	0.10 RPM	106.59 RPM
SRP007412_liver	0.03 RPM	54.31 RPM
SRP007412_testis	0.21 RPM	23.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1580 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1580 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2235
Gorilla gorilla	retro_ggor_1667

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Cavia porcellus	ENSCPOG00000006844	4 retrocopies	retro_cpor_158, retro_cpor_539, retro_cpor_605, retro_cpor_660,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mustela putorius furo	ENSMPUG00000017045	1 retrocopy	retro_mputfur_1409,
Pan troglodytes	ENSPTRG00000002807	12 retrocopies	retro_ptro_1082, retro_ptro_1580 , retro_ptro_1645, retro_ptro_1755, retro_ptro_2080, retro_ptro_2361, retro_ptro_2889, retro_ptro_2890, retro_ptro_3114, retro_ptro_3238, retro_ptro_634, retro_ptro_714,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sus scrofa	ENSSSCG00000010517	1 retrocopy	retro_sscr_373,
Ictidomys tridecemlineatus	ENSSTOG00000025955	1 retrocopy	retro_itri_1187,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,