RetrogeneDB ID: retro_rnor_2361

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:54812827..54813267(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pgam1
• Ensembl ID: ENSRNOG00000050585
• Aliases: Pgam1, Pgmut
• Description: Phosphoglycerate mutase 1 [Source:UniProtKB/Swiss-Prot;Acc:P25113]

Sequence

>retro_rnor_2361
GCTAAGCATGGTGAGGCACATGCTAAGCATGGAGACCATCTTACAATGTCCTGTCGCCTCCAATGGAGCCTGGTCATCCC
TTCTACAGCAACATCAACAAAGATTTCAGATACACAGACATTACTGAGAACCAGCTACCCTCCTGTGAGAGCCTGAAGGA
CACCATTGCCAGAGACTTCTAGAATGAAGAAATTGTCCCCCAGATGAAGGTGGGGAAAAGGTCTTGATTACTGCTATTGC
AACAGCCCTTGGAGCATCATCAATCATCTGAAGGGTCTCTTAGAAGAAGACATTATGGAGCTGAACCTGCCAATGGGCAT
TCCCATCAACTATGACTAGGACAGGACTTGAAGCCCATCAATCCCATGTAGTTCCTGGAAGATGGGGGGACCTTAAGTAA
AGCTATGGAAGCTGTGGCTGCACAGGGTAAGGTGAAGAAA

Alignment

ORF - retro_rnor_2361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.48 %
• Parental protein coverage: 59.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AKHGEAQVK-IWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARALPFWNEEIVP
          AKHGEA..K..WR.SY.V..PPMEP.HPFYSNI.KD.RY.D.TE.QLPSCESLKDTIAR...F.NEEIVP
Retrocopy AKHGEAHAK<AWRPSYNVLSPPMEPGHPFYSNINKDFRYTDITENQLPSCESLKDTIAR--DF*NEEIVP

Parental  QIKEGKR-VLIAA-HGNSLRGIVKHLEGLSEEAIMELNLPTGIPIVYE-LDKNLKPIKPMQFLGDEETVR
          Q.K.GKR.VLI.A...NS...I..HL.GL.EE.IMELNLP.GIPI.Y..L...LKPI.PM.FL.D..T..
Retrocopy QMKVGKR<VLITA<YCNSPWSIINHLKGLLEEDIMELNLPMGIPINYD<LGQDLKPINPM*FLEDGGTLS

Parental  KAMEAVAAQGKVKK
          KAMEAVAAQGKVKK
Retrocopy KAMEAVAAQGKVKK

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
SRP017611_brain	0.00 RPM	415.99 RPM
SRP017611_kidney	0.00 RPM	327.21 RPM
SRP017611_liver	0.00 RPM	111.75 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2361 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2361 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 108 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012697	2 retrocopies	retro_btau_1611, retro_btau_472,
Canis familiaris	ENSCAFG00000009062	1 retrocopy	retro_cfam_1297,
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,
Erinaceus europaeus	ENSEEUG00000005630	1 retrocopy	retro_eeur_680,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
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,
Microcebus murinus	ENSMICG00000007657	1 retrocopy	retro_mmur_135,
Myotis lucifugus	ENSMLUG00000009117	6 retrocopies	retro_mluc_1280, retro_mluc_1595, retro_mluc_1741, retro_mluc_2246, retro_mluc_632, retro_mluc_745,
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,
Mus musculus	ENSMUSG00000011752	6 retrocopies	retro_mmus_1741, retro_mmus_2221, retro_mmus_3012, retro_mmus_411, retro_mmus_729, retro_mmus_769,
Nomascus leucogenys	ENSNLEG00000013804	10 retrocopies	retro_nleu_1367, retro_nleu_1535, retro_nleu_1658, retro_nleu_2012, retro_nleu_2139, retro_nleu_2196, retro_nleu_2205, retro_nleu_2488, retro_nleu_2667, retro_nleu_280,
Oryctolagus cuniculus	ENSOCUG00000005679	5 retrocopies	retro_ocun_1016, retro_ocun_1081, retro_ocun_350, retro_ocun_706, retro_ocun_976,
Pongo abelii	ENSPPYG00000002530	9 retrocopies	retro_pabe_1325, retro_pabe_2309, retro_pabe_2554, retro_pabe_2639, retro_pabe_2881, retro_pabe_3389, retro_pabe_3639, retro_pabe_3749, retro_pabe_671,
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	ENSRNOG00000013532	1 retrocopy	retro_rnor_2889,
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,
Sarcophilus harrisii	ENSSHAG00000018230	1 retrocopy	retro_shar_323,
Sus scrofa	ENSSSCG00000010517	1 retrocopy	retro_sscr_373,
Ictidomys tridecemlineatus	ENSSTOG00000025955	1 retrocopy	retro_itri_1187,
Tupaia belangeri	ENSTBEG00000005913	5 retrocopies	retro_tbel_1677, retro_tbel_1708, retro_tbel_2756, retro_tbel_3667, retro_tbel_563,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,