RetrogeneDB ID: retro_btau_1373

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:30666745..30667505(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.20216
• Ensembl ID: ENSBTAG00000002866
• Aliases: None
• Description: Ribose-5-phosphate isomerase [Source:UniProtKB/Swiss-Prot;Acc:Q3T186]

Sequence

>retro_btau_1373
CAGCTCGGCCCTGGCAGCACAAGTACCCGGGGCAAGGAGGTTAACAACCTCTGCCTGGGCCCTTCCACGATGTCAAAGGC
GGAGGAGGCCAAGAAGCTGGCAGGCTGCGCCGTGGCAGAGAAGGAGGTGAGGAATAACCAAGTGCTGGGAACTGGTAGTG
ACTCTACAATTGTCCACGCAGTGCAACGAATAGCTAAAAGAGTGAAACGAGGGAATCGGAACCACGTTTGTATTCCCACT
TCCTTCCAGGCCCATCAGCTTATCCTACAGTATGACTTACCTCTCAGTGAACCAGAGATCCGCCACACCATCAATGGTGC
TGATGAAGTAGATGCAGACCTCAACCTCACAAGGGCGGTGGAGGCCACCTCACCCAGAAAATTGTGGCCGGCAAAGCCAT
CCGTTTCATTGTGATCTCTGATTTTAGGAAAGATTCAAAGAACCTCGGGAATCAGTGGCACAAGGGGATTCCCATCGAGG
TCATCCGATGGCCTATGTCGCAGTGAGCTGAACCGGGACCCAGAAGTTTGGGGGTGCGATTTAACTTCCACTGGCTGTCA
ACAAGGCAGGTTGTGTGGTGAGGGATAATGGGAACTTTATCCTGGACTGGAAGTTTGACCAGGTCCACAAATGGAGTAAA
GTGAACACAGCTATCAAAATGATCCCAGGCATGCTGGACATGGGCCTGTTCATCAACATATTGGAGAGACCCTACTTTGG
GATGTAGAACAGCTTGGTGAACAGGAGGGAGAAGCTGTTC

Alignment

ORF - retro_btau_1373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.56 %
• Parental protein coverage: 84.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QFGAGSTSTGVRETNIVCPGPSAMSKAEEAKKLAGRAAVENHVRNNQVLGIGSGSTIVHAVQRIAERVEQ
          Q.G.GSTST...E.N..C.GPS.MSKAEEAKKLAG.A..E..VRNNQVLG.GS.STIVHAVQRIA.RV..
Retrocopy QLGPGSTSTRGKEVNNLCLGPSTMSKAEEAKKLAGCAVAEKEVRNNQVLGTGSDSTIVHAVQRIAKRVKR

Parental  ENLKLVCIPTSFQARQLILQYGLTLSDLDRHPEIDLAIDGADEVDADLNLI-KGGGGCLTQEKIVAGNAS
          .N...VCIPTSFQA.QLILQY.L.LS.....PEI...I.GADEVDADLNL..KGGGG.LTQ.KIVAG.A.
Retrocopy GNRNHVCIPTSFQAHQLILQYDLPLSE----PEIRHTINGADEVDADLNLT<KGGGGHLTQ-KIVAGKAI

Parental  RFIVIADFRKDSKNLGDQWHKGIPIEVI-PMAYVPVSRTVTQKFGGVIELRMAVNKAGPVVTDNGNFILD
          RFIVI.DFRKDSKNLG.QWHKGIPIEVI.PMAYV.VS.T.TQKFGG.I.L..AVNKAG.VV.DNGNFILD
Retrocopy RFIVISDFRKDSKNLGNQWHKGIPIEVI<PMAYVAVS*TGTQKFGGAI*LPLAVNKAGCVVRDNGNFILD

Parental  WKFDRVHKWSEVNIAIKMIPGVVDTGLFINMAERVYFGMQDGSVNMREKPF
          WKFD.VHKWS.VN.AIKMIPG..D.GLFIN..ER.YFGM....VN.REK.F
Retrocopy WKFDQVHKWSKVNTAIKMIPGMLDMGLFINILERPYFGM*NSLVNRREKLF

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	0.07 RPM	1.87 RPM
ERP005899_muscle	0.00 RPM	15.41 RPM
SRP017611_brain	0.23 RPM	2.10 RPM
SRP017611_kidney	0.06 RPM	5.75 RPM
SRP017611_liver	0.00 RPM	4.68 RPM
SRP030211_testis	0.17 RPM	23.53 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1373 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1373 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002866	1 retrocopy	retro_btau_1373 ,
Equus caballus	ENSECAG00000011754	1 retrocopy	retro_ecab_645,
Macropus eugenii	ENSMEUG00000008256	1 retrocopy	retro_meug_1506,
Microcebus murinus	ENSMICG00000006462	1 retrocopy	retro_mmur_722,
Myotis lucifugus	ENSMLUG00000005384	1 retrocopy	retro_mluc_1129,
Monodelphis domestica	ENSMODG00000009649	1 retrocopy	retro_mdom_320,
Oryctolagus cuniculus	ENSOCUG00000006840	3 retrocopies	retro_ocun_1541, retro_ocun_1708, retro_ocun_1709,
Otolemur garnettii	ENSOGAG00000034178	2 retrocopies	retro_ogar_1218, retro_ogar_518,
Tarsius syrichta	ENSTSYG00000006406	8 retrocopies	retro_tsyr_1081, retro_tsyr_1088, retro_tsyr_1902, retro_tsyr_2028, retro_tsyr_393, retro_tsyr_709, retro_tsyr_725, retro_tsyr_994,
Tursiops truncatus	ENSTTRG00000000876	2 retrocopies	retro_ttru_1175, retro_ttru_799,