RetrogeneDB ID: retro_btau_172

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:93374422..93375415(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000039540
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC25A3
• Ensembl ID: ENSBTAG00000012890
• Aliases: SLC25A3, D1S155E
• Description: Phosphate carrier protein, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P12234]

Sequence

>retro_btau_172
ATGTGTGATGCTGGCGGTTACCAAGCCCTGCGGGGGAGAAGCGCGGGCCAACTCAATGGCAGGCCCTGGGCAGCAGCCTT
GGAGGAGTCCAGCTACGAGTACGGTTCCACGAAGTACCTACTGCTGTGTGGCCTGGGCGGGATGCTGAGCTGCGGACTGA
CGCACACGGCCATCGTGCCTCTGGACCTGGTCAAGTGTCGCATGCAGGTGGACCCCAGCAAGTACAAGGGCATCCTGAGC
GGCTTTGGCGTGACACTGCGGGACGACGGGCTGCGTGGCCTGGCCCGAGGCTGGGCCCCGACCTTTCTAGGCTACTCCAT
GCAGGGCCTCTTCAAGTTTGGCCTCTACGAGGTCTTCAAAATCCGGTACGCGGAGCTCCTGGGCCAGGAGAAGGCCTACG
AATGGAGAACCGGGCTGTACCTGGCCGCCTCAGCCAGCGCTGAGTTCTTCGCCGACGTGGCCCTGGCCCCGATGGAAGCG
GTGAAGGTTCGCATGCAGACGCAGCAGGGCTATGCCCGCACGCTCCGGGCCGCGGCCCCCAAGATGTACGGCGAGGAGGG
CCTGTGGGCCTTCTACAAAGGCGTGGCGCCGCTCTGGATGCGCCAGATCCCCTATACCATGATGAAGTTCGCCTGCTTCG
AGCGCACGGTCGAGGCGCTTTACAAGTACGTGGTGCCCAAGCCGCAGAGCCATTGCACCAAGAGTGAGCAGCTGGCCGTG
ACCTTTGTGGCCGGCTACATTGCTGGCGTCTTCTGCGCCGTGGTGTCCCACCCTGCGGATTCCGTCGTGTCCGTTTTGAA
CAAGGAGAAAGGCAGCACGGCCTTTGACGTTCTCCAGAGACTGGGGTTCAAGGGCGTGTGGAAAGGCCTGTTCGCCCGGA
TCATCATGATTGGCACCCTGACTGCCCTGCAGTGGTTCATCTACGACTCGGTCAAGGTCTATTTCAAGTTGCCTCGCCCT
CCAGTCCCTCAAGCGCCCAAATCCCGAAAGTAG

Alignment

ORF - retro_btau_172 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.11 %
• Parental protein coverage: 85.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAVEEYSCEYGSAKFYALCGFGGVLSCGLTHTAVVPLDLVKCRMQVDPQKYKSIFNGFSVTLKEDGFRG
          AAA.EE.S.EYGS.K...LCG.GG.LSCGLTHTA.VPLDLVKCRMQVDP.KYK.I..GF.VTL..DG.RG
Retrocopy AAALEESSYEYGSTKYLLLCGLGGMLSCGLTHTAIVPLDLVKCRMQVDPSKYKGILSGFGVTLRDDGLRG

Parental  LAKGWAPTFIGYSLQGLCKFGFYEVFKVLYSNMLGEENAYLWRTSLYLAASASAEFFADIALAPMEAAKV
          LA.GWAPTF.GYS.QGL.KFG.YEVFK..Y...LG.E.AY.WRT.LYLAASASAEFFAD.ALAPMEA.KV
Retrocopy LARGWAPTFLGYSMQGLFKFGLYEVFKIRYAELLGQEKAYEWRTGLYLAASASAEFFADVALAPMEAVKV

Parental  RIQTQPGYANTLRDAAPKMYKEEGLKAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRSECS
          R.QTQ.GYA.TLR.AAPKMY.EEGL.AFYKGVAPLWMRQIPYTMMKFACFERTVEALYK.VVPKP.S.C.
Retrocopy RMQTQQGYARTLRAAAPKMYGEEGLWAFYKGVAPLWMRQIPYTMMKFACFERTVEALYKYVVPKPQSHCT

Parental  KPEQLVVTFVAGYIAGVFCAIVSHPADSVVSVLNKEKGSSASEVLKRLGFRGVWKGLFARIIMIGTLTAL
          K.EQL.VTFVAGYIAGVFCA.VSHPADSVVSVLNKEKGS.A..VL.RLGF.GVWKGLFARIIMIGTLTAL
Retrocopy KSEQLAVTFVAGYIAGVFCAVVSHPADSVVSVLNKEKGSTAFDVLQRLGFKGVWKGLFARIIMIGTLTAL

Parental  QWFIYDSVKVYFRLPRPPPPEMPESLK
          QWFIYDSVKVYF.LPRPP.P..P.S.K
Retrocopy QWFIYDSVKVYFKLPRPPVPQAPKSRK

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	68.56 RPM
ERP005899_muscle	0.00 RPM	226.47 RPM
SRP017611_brain	0.05 RPM	148.09 RPM
SRP017611_kidney	0.41 RPM	314.85 RPM
SRP017611_liver	0.00 RPM	93.78 RPM
SRP030211_testis	20.48 RPM	39.92 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_172 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_172 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013232	1 retrocopy	retro_acar_35,
Bos taurus	ENSBTAG00000012890	1 retrocopy	retro_btau_172 ,
Canis familiaris	ENSCAFG00000006545	1 retrocopy	retro_cfam_880,
Callithrix jacchus	ENSCJAG00000002392	2 retrocopies	retro_cjac_3315, retro_cjac_812,
Dipodomys ordii	ENSDORG00000011431	1 retrocopy	retro_dord_321,
Equus caballus	ENSECAG00000015135	1 retrocopy	retro_ecab_481,
Echinops telfairi	ENSETEG00000012678	1 retrocopy	retro_etel_1748,
Homo sapiens	ENSG00000075415	1 retrocopy	retro_hsap_392,
Gorilla gorilla	ENSGGOG00000015886	1 retrocopy	retro_ggor_394,
Latimeria chalumnae	ENSLACG00000007024	1 retrocopy	retro_lcha_4,
Macropus eugenii	ENSMEUG00000016593	2 retrocopies	retro_meug_405, retro_meug_658,
Microcebus murinus	ENSMICG00000003520	1 retrocopy	retro_mmur_298,
Myotis lucifugus	ENSMLUG00000008330	1 retrocopy	retro_mluc_1184,
Macaca mulatta	ENSMMUG00000023036	1 retrocopy	retro_mmul_496,
Monodelphis domestica	ENSMODG00000007717	2 retrocopies	retro_mdom_2026, retro_mdom_293,
Mus musculus	ENSMUSG00000061904	1 retrocopy	retro_mmus_1959,
Nomascus leucogenys	ENSNLEG00000005973	1 retrocopy	retro_nleu_2402,
Oryctolagus cuniculus	ENSOCUG00000011847	1 retrocopy	retro_ocun_390,
Otolemur garnettii	ENSOGAG00000012222	2 retrocopies	retro_ogar_1816, retro_ogar_2052,
Pongo abelii	ENSPPYG00000004858	1 retrocopy	retro_pabe_1768,
Pan troglodytes	ENSPTRG00000005333	1 retrocopy	retro_ptro_302,
Pteropus vampyrus	ENSPVAG00000005890	1 retrocopy	retro_pvam_212,
Sorex araneus	ENSSARG00000001149	1 retrocopy	retro_sara_262,
Ictidomys tridecemlineatus	ENSSTOG00000027633	2 retrocopies	retro_itri_485, retro_itri_90,
Tupaia belangeri	ENSTBEG00000014548	1 retrocopy	retro_tbel_1792,
Tursiops truncatus	ENSTTRG00000004739	1 retrocopy	retro_ttru_692,
Vicugna pacos	ENSVPAG00000004704	1 retrocopy	retro_vpac_455,