RetrogeneDB ID: retro_btau_322

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:2928851..2929585(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSBTAG00000020160
• Aliases: None
• Description: E3 ubiquitin-protein ligase RNF138 [Source:UniProtKB/Swiss-Prot;Acc:Q32LN5]

Sequence

>retro_btau_322
ATGGGTGAGGAGCTCTCTGTGGCCTCATCCTATATCAAGGATGTTTTCTTCTGCCCCGTCTGTCAGGAGGTGTTCACAAC
TCCCATGTATACTGTGACCTGTCTGCACGTTTTCTGTAGAAAATGTTTCCTGACTGCAATGAGAGAAAGTGGAATATACT
GTCCCTTCTGTCGTGGAAATGTAACTAGGAGAGAGAGAGAGTGTCCTGAATGGGCCTTAGACCTTGAAAATATCATGAGG
AAATTTTCTGGTAGCTGCAGATGCTGTGCAAAACAGATTCAATTCTATTGCATGAGACATCATTACAAATCTCATAAGAA
GTATTGAGATGAATATGGTGTTTCTTCTGTCATTCCAAACTTTCAGATCTCTCAAAATTCAGTATGGAACAGTAATAAGA
CTGAAACATCCACACCTGACAACACAGAATCTTACCAAGAGAACACAAGCTCTTCTGGGCATCCCACTTTAAAGTGTCCT
TTGTGTCAAGAATCAAATATGATGAGAGAGCATTTCCTGGATCACTGTGACAGTGATCACCTTTCAGAATGCTTCCTGGG
ATGTGTCCTATTTGTGTATCTCTTCCTTGGGTAGATCTAGCCAGATTACTCGAAATTTTGTTAGTCATCGAAATCAAAAG
ACATCAGTTTGATTATGGAGAATTTGTGAATCTTCAGCTAGATGAGGAAACTAGCTATCAAAATGCTGTTGAAGAATCTT
TTAAAATAAACATC

Alignment

ORF - retro_btau_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAEELSAATSYTEDDFYCPVCQEVLKTPVRTAACQHVFCRKCFLTAMRESGIHCPLCRGNVTRRERACPE
          M.EELS.A.SY..D.F.CPVCQEV..TP..T..C.HVFCRKCFLTAMRESGI.CP.CRGNVTRRER.CPE
Retrocopy MGEELSVASSYIKDVFFCPVCQEVFTTPMYTVTCLHVFCRKCFLTAMRESGIYCPFCRGNVTRRERECPE

Parental  RALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSIIPNFQISQDSVGNSNRSETSASD
          .ALDLENIMRKFSGSCRCCAKQI.FY.MRHHYKS.KKY.DEYGVSS.IPNFQISQ.SV.NSN..ETS..D
Retrocopy WALDLENIMRKFSGSCRCCAKQIQFYCMRHHYKSHKKY*DEYGVSSVIPNFQISQNSVWNSNKTETSTPD

Parental  NIETYQENTGSSGHPTFKCPLCQESNFTRQRLLDHCNSNHL-FQIVPVTCPICVSLPW-GDPSQVTRNFV
          N.E.YQENT.SSGHPT.KCPLCQESN..R...LDHC.S.HL.F...P..CPICVSLPW.G..SQ.TRNFV
Retrocopy NTESYQENTSSSGHPTLKCPLCQESNMMREHFLDHCDSDHL<FRMLPGMCPICVSLPW<GRSSQITRNFV

Parental  SHLNQ-RHQFDYGEFVNLQLDEETQYQTAVEESFQVNI
          SH.NQ.RHQFDYGEFVNLQLDEET.YQ.AVEESF..NI
Retrocopy SHRNQ>RHQFDYGEFVNLQLDEETSYQNAVEESFKINI

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	3.75 RPM
ERP005899_muscle	0.11 RPM	4.12 RPM
SRP017611_brain	0.09 RPM	4.16 RPM
SRP017611_kidney	0.00 RPM	4.74 RPM
SRP017611_liver	0.00 RPM	2.49 RPM
SRP030211_testis	0.02 RPM	71.27 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_322 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_322 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_322 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020160	1 retrocopy	retro_btau_322 ,
Choloepus hoffmanni	ENSCHOG00000012689	6 retrocopies	retro_chof_1043, retro_chof_1242, retro_chof_1931, retro_chof_418, retro_chof_714, retro_chof_793,
Callithrix jacchus	ENSCJAG00000020875	1 retrocopy	retro_cjac_2325,
Felis catus	ENSFCAG00000014180	2 retrocopies	retro_fcat_1383, retro_fcat_379,
Homo sapiens	ENSG00000134758	1 retrocopy	retro_hsap_3319,
Gorilla gorilla	ENSGGOG00000027857	1 retrocopy	retro_ggor_1302,
Loxodonta africana	ENSLAFG00000003811	1 retrocopy	retro_lafr_408,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mustela putorius furo	ENSMPUG00000006982	1 retrocopy	retro_mputfur_276,
Nomascus leucogenys	ENSNLEG00000006401	1 retrocopy	retro_nleu_1665,
Pongo abelii	ENSPPYG00000009094	1 retrocopy	retro_pabe_2734,
Pan troglodytes	ENSPTRG00000009956	1 retrocopy	retro_ptro_2155,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Rattus norvegicus	ENSRNOG00000015645	3 retrocopies	retro_rnor_2316, retro_rnor_808, retro_rnor_965,
Ictidomys tridecemlineatus	ENSSTOG00000002293	2 retrocopies	retro_itri_1443, retro_itri_576,