RetrogeneDB ID: retro_btau_1413

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:31710491..31711422(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLUD1
• Ensembl ID: ENSBTAG00000007540
• Aliases: GLUD1, GDH
• Description: Glutamate dehydrogenase 1, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P00366]

Sequence

>retro_btau_1413
TCCATCCCCATCCTGCGCCAGTACGGCTCCTGGGAGGTCAGTGAGGGCTACTGGGTCCAGCAGAGCTTAGCATTGCACAC
CCTGCAAAGTAAGTATTGGTTAGTGAGAAGATGTGAGTGCAGATAAAGTAAAAGCTTTGGTTTGCCTGCTGACGTATAAA
TGTGCTATGTTGATGTGCCATTTGGCAGTGCTAAAGCTGATGTTAAGATCAATCCCAGGAACCAGACTGATAATTAAGTG
GAAAAGATCACAAGGAATTCACCATGGAGCTGGAAAAACAGAGCTTTATTGATCCCGGCATTGATGTGCCTTCCCCAGTC
AGGGCCACAGGTGAGTGAGAAAATGTCCTGGATTGCTGATACCTGTGACAGCACCGTTGGGCACTGAGATATTAATGCAC
ATCCCTGCTATTACTGGTAAATCCATCAGTCAGAGTGGCATCCACAGAGGTATCTCTGCCACTGGTAATGGTGTTTGCCA
TGGGATTGAAAATTTCCTCAGTGAAGTTTCTTACACAAGCATTTTACGAATACACCGGGATTTGGAGATAAAACATTTCT
TTCCAGAGATTTGGTAATGTGGGCCTATACTGTATGGCATATTTACATCATATTGGTGCTAAATGTGTTGATGGTGGTGA
AGTTGATGGTAGCACATGAAATTCAGATGGCACTGACCCAAAGGAACTAGAAGACTACAAATTGCAACATGAATCAATTC
TGGACTTCCCCAAGGCAAAACCCTTGGAAGGAAGCATCTTGGAAGCAGACTGTGACATACCAGTCCCTGCAGCCAATGAG
AAGCAGTTGACCAAATCCAGTGCATTGAAAGCAAGATCATTGCTGAAGCTGCCAGTGGGTCAACAACTCCAGAACCTTAG
TTTTTTCTGGGGAAGAACAGTATGGTTATTTCTGATCTCTACATGAATGCT

Alignment

ORF - retro_btau_1413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.08 %
• Parental protein coverage: 55.97 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  SFPIRRDDGSWEVIEGYRAQHSQ-HRTPCKGGIRYSTDVSVDEVKALASLMTYKCAV-VDVPFGGAKAGV
          S.PI.R..GSWEV.EGY..Q.S..H.TPCK..I....DVS.D.VKAL..L.TYKCA..VDVPFG.AKA.V
Retrocopy SIPILRQYGSWEVSEGYWVQQSL>HCTPCKVSIG**EDVSADKVKALVCLLTYKCAM<VDVPFGSAKADV

Parental  KINPKNYTDNELEKITRR-FTMELAKKGFIGPGVDVPAPDMSTGERE-MSWIADTYASTIGHYDINAHAC
          KINP.N.TDN..EKITR..FTMEL.K..FI.PG.DVP.P...TGE.E.MSWIADT..ST.GH.DINAH.C
Retrocopy KINPRNQTDN*VEKITRN<FTMELEKQSFIDPGIDVPSPVRATGE*E>MSWIADTCDSTVGH*DINAHPC

Parental  -VTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGM-TPGFGDKTF-AVQGFGNVGLHSMRYLH
          ..TGK.ISQ.GIH..ISATG.GV.HGIENF..E.SY.SIL...TPGFGDKTF...Q.FGNVGL..M.YLH
Retrocopy >ITGKSISQSGIHRGISATGNGVCHGIENFLSEVSYTSILRI<TPGFGDKTF<SFQRFGNVGLYCMAYLH

Parental  RFGAKCVAVGESDGSIWNPDGIDPKELEDFKLQHGTILGFPKAKIYEGSILEVDCDILIPAASEKQLTKS
          ..GAKCV..GE.DGS..N.DG.DPKELED.KLQH..IL.FPKAK..EGSILE.DCDI..PAA.EKQLTKS
Retrocopy HIGAKCVDGGEVDGST*NSDGTDPKELEDYKLQHESILDFPKAKPLEGSILEADCDIPVPAANEKQLTKS

Parental  NAPRVKA-KIIAEGANGPTTPEADKIFLERNIMVIPDLYLNA
          .A...KA.KIIAE.A.G.TTPE....FL..N.MVI.DLY.NA
Retrocopy SA--LKA<KIIAEAASGSTTPE-P*FFLGKNSMVISDLYMNA

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	587.87 RPM
ERP005899_muscle	0.00 RPM	304.01 RPM
SRP017611_brain	0.00 RPM	299.47 RPM
SRP017611_kidney	0.06 RPM	649.08 RPM
SRP017611_liver	0.00 RPM	571.37 RPM
SRP030211_testis	0.12 RPM	28.05 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1413 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1413 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1413 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413 , retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,