RetrogeneDB ID: retro_itri_1187

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393395.1:5328137..5328658(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM1
• Ensembl ID: ENSSTOG00000025955
• Aliases: None
• Description: phosphoglycerate mutase 1 (brain) [Source:HGNC Symbol;Acc:8888]

Sequence

>retro_itri_1187
AATGCCGGTGACCAGATGTGGCTGCCAGTGCTGAAAACTGGGCACCCCAATGATGAAGATCTAACTGTCCTCAACAACGC
CAAAACTGCTGCAAAGCTTTGGGAGTCCCAGGTAGAGATCTGAAGGTGTTCCCAGGATGATTTAGCACCTCAATGGAGCC
TGGCCATTCCTCTACAGCAGTATCAGTAAAGTCATCTCAGTATGTAGACTTCACAGAAGGTGAGCTACTCTCCTGTGTGG
GTCTATAGGAAGCTAGGAGTTCCCTACCCTTTTGGAATGAAGAAAGAGTTCCCCAAATCCAGAAGGGGAAATAGATCCTG
ATTGCCGCTCATGGAAAAAGCCTTTGGGGCACTGGTAAGCATCTGGAGGGCATCTCTAAAGAAGCCATCATAAAGCTGAA
CCTGCCAATTTGTATTCTCATTGTCTATGAATTGAATAAGAAATTTAAATCCATCAAGCCAGTGTAATTCCTGGAAGATG
GAAAGACCTTGTGTAAAGCCATAGAAGTTATGGCTGTCAGA

Alignment

ORF - retro_itri_1187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.51 %
• Parental protein coverage: 70.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPP-MEPDHPFYSNISKDR
          .A.DQMWLPV..T...N......LT.LN.A.TAAK..E.QV.I.R.S.D...P..MEP.H.......K..
Retrocopy NAGDQMWLPVLKTGHPNDED---LTVLNNAKTAAKLWESQVEI*RCSQDDLAPQ<MEPGHSSTAVSVKSS

Parental  RYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNL
          .Y.D.TE..L.SC..L.......LPFWNEE.VPQI..GK..LIAAHG.SL.G..KHLEG.S.EAI..LNL
Retrocopy QYVDFTEGELLSCVGL*EARS-SLPFWNEERVPQIQKGK*ILIAAHGKSLWGTGKHLEGISKEAIIKLNL

Parental  PTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQ
          P..I.IVYEL.K..K.IKP..FL.D..T..KA.E..A..
Retrocopy PICILIVYELNKKFKSIKPV*FLEDGKTLCKAIEVMAVR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1187 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1187 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,