RetrogeneDB ID: retro_btau_1611

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:48263174..48263861(+)
• Located in intron of: ENSBTAG00000005090

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM1
• Ensembl ID: ENSBTAG00000012697
• Aliases: None
• Description: Phosphoglycerate mutase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ62]

Sequence

>retro_btau_1611
ATGGCTGCCTACAAGCTGGTGCTGATCCGGCACGGTGAGAGCACATGGAACCTGGAGAACCGTTTCAGCGGCTGGTAGGA
CGCGGACCTGAGCCTAGCCGGGCATGAGGAGGCGAAGCGAGGCAGGCAGGCGCTGAGAGATGCTGGCTATGAGTTTGACA
TCTGCTTCACCTCAGTGCAGAAGAGAGCAATCCGGATCCTCTGGACAGTGCTGGATGCCATCGACCAAATGTGGCTGCCA
GTGGTGAGGACTTGGCGCCTTAATGAGCGACACTATGGGGGTCTGACTGGCCTCAATAAGGCAGAAACTGCTGCCAAGCA
TGGTGAGGCCCAGGTAAAGATCTGGAGGTGCTCCTATGATGTCCCGCCACCTCCCATGGAGCCCGACCATCCCTTCTATA
GCAACATCAGTAAGGATCACAGGTACACAGACCTCACTGAAGACCAGCTGCCCTCCTGTGAGAGTCTGAAGGACACAATT
GCCAGAGCTCTGCCCTTTTGGAATGAAGAAATTGTCCCCCAGATCAAGGAGGTGAAAAGGGTACTAATTGTAGCCCATGG
CAACAGCCTTTGGCGCATCGTCAAGCATCTGGAGGGTCTCTCTGAAGAGGCTATCATGGAGCTGAACCTGCCAACTGGCA
TTCCCATGGTCTATGAGTTGGACAAGAACTTGAAGCCCATCAAGCCA

Alignment

ORF - retro_btau_1611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.2 %
• Parental protein coverage: 90.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAYKLVLIRHGESTWNLENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTV
          MAAYKLVLIRHGESTWNLENRFSGW.DADLS.AGHEEAKRG.QALRDAGYEFDICFTSVQKRAIR.LWTV
Retrocopy MAAYKLVLIRHGESTWNLENRFSGW*DADLSLAGHEEAKRGRQALRDAGYEFDICFTSVQKRAIRILWTV

Parental  LDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDR
          LDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWR.SYDVPPPPMEPDHPFYSNISKD.
Retrocopy LDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRCSYDVPPPPMEPDHPFYSNISKDH

Parental  RYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIMELNL
          RY.DLTEDQLPSCESLKDTIARALPFWNEEIVPQIKE.KRVLI.AHGNSL..IVKHLEGLSEEAIMELNL
Retrocopy RYTDLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEVKRVLIVAHGNSLWRIVKHLEGLSEEAIMELNL

Parental  PTGIPMVYELDKNLKPIKP
          PTGIPMVYELDKNLKPIKP
Retrocopy PTGIPMVYELDKNLKPIKP

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
ERP005899_liver	0.00 RPM	33.52 RPM
ERP005899_muscle	0.00 RPM	176.26 RPM
SRP017611_brain	0.09 RPM	252.70 RPM
SRP017611_kidney	0.18 RPM	166.02 RPM
SRP017611_liver	0.08 RPM	96.50 RPM
SRP030211_testis	0.00 RPM	40.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1611 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1611 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 79 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,
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,
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,
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,
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,