RetrogeneDB ID: retro_btau_323

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:4190195..4190875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK3
• Ensembl ID: ENSBTAG00000017147
• Aliases: AK3, AK3L1
• Description: GTP:AMP phosphotransferase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P08760]

Sequence

>retro_btau_323
ATGGGGCCATCGAGGCAGCTCCTGCACTCCCGTGATCGTGGGTGCCGCGGGCTCCGGCAAGTGTACCCTGGCACTGCTCA
TTACCAAACACTTCCAGCTGAAGACCTTCTCCAGTGGGCATGTGATCCGAGACAACATGTGAAGGGACACAGAAATCAGG
GTGCTGGCCAAGACCTTCATGGACCAGGGGAAGCTCATCCCGGACAACCTCATTATTCGGCTGTTGCTCCAGAAGCTGAA
AAATGCCATCCAGTATAACTGGCTGTTATGTGGTTTCCCCAGGACACTTGCACAGGCTGAAGCCCTGGACAGAGTCCATC
AGGTACACTCGGTGATGAACCTGAATGTACCATTTGAGGTCATTGGCATCGCCTCGAGGCTCGCTGGGTTCATCCAGCCA
GTGGCCGCGTCTATAACCTCAGATTTAACCCTCCCAAAGTGGTCGGTGTGGACGATGTGACTGGAAAGCCTCTCATTCAG
CCTGTAGACAATAAATCTGAGACACTTAGCAAAAGAATGAAGGTTTACCAAGACCAAACGAAACCGGTCCTGGAATATTA
TCAGAAAAAGGGAGTATTGGAAACATTTTCTGGAACAGAAACCAGTAAGATCTGGCCCTGTATGCAGGCTTTCCTGCAAA
CCAAAGTCCCACTGAGACACCCAAAAACTCAGTTACTCCA

Alignment

ORF - retro_btau_323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGASARLLRA-AIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLAKTFIDQGKLIPDD
          MG.S..LL....I.GA.GSGK.T....ITKHF.LK..SSG...RDNM.R.TEI.VLAKTF.DQGKLIPD.
Retrocopy MGPSRQLLHS>VIVGAAGSGKCTLALLITKHFQLKTFSSGHVIRDNM*RDTEIRVLAKTFMDQGKLIPDN

Parental  VMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIK-QRLTARWIHPGSGRVY
          ...RL.L..LKN..QYNWLL.GFPRTL.QAEALDR..Q...V.NLNVPFEVI...RL.ARW.HP.SGRVY
Retrocopy LIIRLLLQKLKNAIQYNWLLCGFPRTLAQAEALDRVHQVHSVMNLNVPFEVIG<HRLEARWVHPASGRVY

Parental  NIEFNPPKTMGIDDLTGEPLVQREDDRPETVVKRLKAYEAQTEPVLEYYRKKGVLETFSGTETNKIWPHV
          N..FNPPK..G.DD.TG.PL.Q..D...ET..KR.K.Y..QT.PVLEYY.KKGVLETFSGTET.KIWP..
Retrocopy NLRFNPPKVVGVDDVTGKPLIQPVDNKSETLSKRMKVYQDQTKPVLEYYQKKGVLETFSGTETSKIWPCM

Parental  YAFLQTKLPQRSQET-SVTP
          .AFLQTK.P.R...T.SVTP
Retrocopy QAFLQTKVPLRHPKT<SVTP

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	132.58 RPM
ERP005899_muscle	0.00 RPM	123.90 RPM
SRP017611_brain	0.00 RPM	23.07 RPM
SRP017611_kidney	0.00 RPM	255.05 RPM
SRP017611_liver	0.00 RPM	68.34 RPM
SRP030211_testis	0.04 RPM	35.46 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_323 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_323 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_317
Callithrix jacchus	retro_cjac_1940

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002640	3 retrocopies	retro_amel_1009, retro_amel_1916, retro_amel_1931,
Bos taurus	ENSBTAG00000017147	1 retrocopy	retro_btau_323 ,
Bos taurus	ENSBTAG00000030674	1 retrocopy	retro_btau_782,
Callithrix jacchus	ENSCJAG00000011188	1 retrocopy	retro_cjac_1940,
Equus caballus	ENSECAG00000011235	2 retrocopies	retro_ecab_317, retro_ecab_914,
Echinops telfairi	ENSETEG00000000829	1 retrocopy	retro_etel_57,
Felis catus	ENSFCAG00000028063	2 retrocopies	retro_fcat_162, retro_fcat_1982,
Homo sapiens	ENSG00000147853	3 retrocopies	retro_hsap_1163, retro_hsap_3228, retro_hsap_555,
Gorilla gorilla	ENSGGOG00000028122	3 retrocopies	retro_ggor_2195, retro_ggor_503, retro_ggor_908,
Loxodonta africana	ENSLAFG00000001126	1 retrocopy	retro_lafr_205,
Microcebus murinus	ENSMICG00000013112	3 retrocopies	retro_mmur_1474, retro_mmur_1559, retro_mmur_1579,
Myotis lucifugus	ENSMLUG00000017272	1 retrocopy	retro_mluc_535,
Macaca mulatta	ENSMMUG00000000143	2 retrocopies	retro_mmul_2032, retro_mmul_898,
Mustela putorius furo	ENSMPUG00000005006	2 retrocopies	retro_mputfur_1163, retro_mputfur_890,
Nomascus leucogenys	ENSNLEG00000008885	3 retrocopies	retro_nleu_2638, retro_nleu_2653, retro_nleu_948,
Oryctolagus cuniculus	ENSOCUG00000011411	1 retrocopy	retro_ocun_716,
Otolemur garnettii	ENSOGAG00000007477	2 retrocopies	retro_ogar_3482, retro_ogar_3492,
Pongo abelii	ENSPPYG00000019245	3 retrocopies	retro_pabe_2676, retro_pabe_3588, retro_pabe_967,
Pan troglodytes	ENSPTRG00000020742	5 retrocopies	retro_ptro_1785, retro_ptro_2180, retro_ptro_2895, retro_ptro_416, retro_ptro_796,
Pteropus vampyrus	ENSPVAG00000015751	1 retrocopy	retro_pvam_269,
Sus scrofa	ENSSSCG00000023595	1 retrocopy	retro_sscr_641,
Ictidomys tridecemlineatus	ENSSTOG00000000021	1 retrocopy	retro_itri_933,
Tupaia belangeri	ENSTBEG00000008054	3 retrocopies	retro_tbel_1463, retro_tbel_3247, retro_tbel_3397,
Tursiops truncatus	ENSTTRG00000016524	1 retrocopy	retro_ttru_1036,
Vicugna pacos	ENSVPAG00000009187	1 retrocopy	retro_vpac_137,