RetrogeneDB ID: retro_btau_1163

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:30410996..30411646(-)
• Located in intron of: ENSBTAG00000011072

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIDA
• Ensembl ID: ENSBTAG00000007593
• Aliases: None
• Description: axin interactor, dorsalization-associated protein [Source:RefSeq peptide;Acc:NP_001192563]

Sequence

>retro_btau_1163
GAAGATCTGAAGAGGCTAGAACCAATCCTAAAGAATATTCTTACATATAATAAAGAACTCCCATTTGATGTTCAGCCTGT
CCCTTTAAGAAGAACTTTAGCACCTGGTGCAGAAGAGAATTCGGAATTTGAAGAAGATGAAGAAGAGGGTGGCACTGGAG
CAGGGTCTCCTGATTTCTTTCCTGCCAGAGCTCCCAGTACTTGATTACCAAGGCTGCCATCAGAACCAGGAACGACGTTA
CTACCAGAATTGAGAAAACTGGCCTGAAAGATGCCAGGCAATGCACTGATCCCTATATCACAGTTAGGGTAAAAGACCTG
AATGGCACAAATTTAACTCCTGTGCAAGATACTCCTGTGGCTTCAAGAACAGGAGATACATATGCTCATTTTAATGTAGA
CATTGAGCTCCAGAAGCATGTTGAAAAATTAACCAAAGGTGCAGCTATTTTTTTTTAATTCAAACACTACAAGCCTAAAG
AAAGGTTTACCAGCACCGAGTGTTTTGCTTTCATGGAGATGGCTGAAATTAAACCTGGGCCAACTGTAACAGAACTATAC
AAGAAACCCACTGACTTTAAAAGAAAGAAATTGCAATTATTGTCCAAGAAAACGTTTTATCTTCATCTGCATCAAACTTT
CCACAAGGAA

Alignment

ORF - retro_btau_1163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.19 %
• Parental protein coverage: 71.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGEEENLEFEEDEEEGGAGAGSPDSFPARVPGTLLP
          EDLK.LEPILKNILTYNKE.PFDVQPVPLRR.LAPG.EEN.EFEEDEEEGG.GAGSPD.FPAR.P.T.LP
Retrocopy EDLKRLEPILKNILTYNKELPFDVQPVPLRRTLAPGAEENSEFEEDEEEGGTGAGSPDFFPARAPST*LP

Parental  RLPSEPGMTLLTIKIEKI-GLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVASRKEDTYVHFNVDIELQ
          RLPSEPG.TLL.....K..GLKDA.QC.DPYITV.VKDLNG..LTPVQDTPVASR..DTY.HFNVDIELQ
Retrocopy RLPSEPGTTLLP-ELRKL<GLKDARQCTDPYITVRVKDLNGTNLTPVQDTPVASRTGDTYAHFNVDIELQ

Parental  KHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLLTKKPLYL
          KHVEKLTKGAA....FKHYKPK.RFTST.CFAFMEM.EIKPGP.V.ELYKKPTDFKRKKLQLL.KK..YL
Retrocopy KHVEKLTKGAAXXXXFKHYKPKERFTSTECFAFMEMAEIKPGPTVTELYKKPTDFKRKKLQLLSKKTFYL

Parental  HLHQTLHKE
          HLHQT.HKE
Retrocopy HLHQTFHKE

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	7.35 RPM
ERP005899_muscle	0.05 RPM	16.79 RPM
SRP017611_brain	0.00 RPM	10.92 RPM
SRP017611_kidney	0.00 RPM	16.06 RPM
SRP017611_liver	0.23 RPM	7.55 RPM
SRP030211_testis	0.00 RPM	13.69 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1163 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1163 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007593	2 retrocopies	retro_btau_1163 , retro_btau_573,
Choloepus hoffmanni	ENSCHOG00000010095	2 retrocopies	retro_chof_1919, retro_chof_97,
Dasypus novemcinctus	ENSDNOG00000008380	5 retrocopies	retro_dnov_1765, retro_dnov_1909, retro_dnov_1961, retro_dnov_2172, retro_dnov_2280,
Homo sapiens	ENSG00000186063	4 retrocopies	retro_hsap_1901, retro_hsap_2076, retro_hsap_2998, retro_hsap_410,
Gorilla gorilla	ENSGGOG00000015289	3 retrocopies	retro_ggor_1394, retro_ggor_1627, retro_ggor_2077,
Macaca mulatta	ENSMMUG00000015025	1 retrocopy	retro_mmul_1918,
Monodelphis domestica	ENSMODG00000004774	3 retrocopies	retro_mdom_1417, retro_mdom_1418, retro_mdom_1448,
Nomascus leucogenys	ENSNLEG00000013583	1 retrocopy	retro_nleu_748,
Oryctolagus cuniculus	ENSOCUG00000017030	1 retrocopy	retro_ocun_688,
Pongo abelii	ENSPPYG00000000196	2 retrocopies	retro_pabe_2015, retro_pabe_2485,
Pan troglodytes	ENSPTRG00000002010	3 retrocopies	retro_ptro_1254, retro_ptro_1528, retro_ptro_2027,
Tarsius syrichta	ENSTSYG00000005745	3 retrocopies	retro_tsyr_101, retro_tsyr_1795, retro_tsyr_514,
Tursiops truncatus	ENSTTRG00000016594	1 retrocopy	retro_ttru_1084,