RetrogeneDB ID: retro_btau_573

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:18342103..18343021(+)
• Located in intron of: None

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_573
ATGTCGGAGGTGACCCGAAGTCTGCTGCTGCGCTGGGGCGCCAGTTTTAGGAGAGGCGCCGACTTCGACTCTTGGGGCCA
GCTGGTGGAGGCGATAGACGAGTATCAGATATTAGCAAGACACCTACAAAAAGAGGCCCAAGCTCAACACAATAATTCTG
AATTCACAGAAGAACAAAAGAAAACCATAGGCAAAATTGCAACACGCTTGGAATTACGAAGTGCAGCTTTACAGTCCACA
CAGTCCCAGGAAGAATTTAAACTGGAAGATCTGAAGAAGCTAGAACCAATCCTAAAGAATATTCTTACATATAATAAAGA
ATTCCCATTTGATGTTCAGCCTGTCCCTTTAAGAAGAATTTTAGCACCTGGTGGAGAAGAGAATTTGGAATTTGAAGAAG
ATGAATAAGAGGGTGGTGCTGGAGCAGGATCTCCTGATTCCTTTCCTGCCAGAGTTCCCGATACTTTATTACCAAGGTTG
CCATCAGAACCAGGAATGATGTTACTCACTATCAAGATTGAGAAAATTGGCCTGAAAGATGCCGGGCAATGCATTGATCC
CTATATCACAGTTAGTGTAAAAGATCTGAATGGCATAGATTTAACTCCTGTGCAAGATACTCCTGTGGCTTCAAGGAAAG
AAGATACGTATGTTCATTTTAATGTGGACATTGAGCTCCAGAAGCATGTTGAAAAGTTAACCAAAGGTGCAGCTATTTTT
TTTGAATTCAAACACTACAAGCCTAAAAAAAGGTTTACCAGCACCAAGTGTTTTGCTTTCATGGAGATGGATGAAATTAA
ACCTGGGCCAATTGTAATAGAACTATACAAGAAACCCACTGACTTTAAAAGAAAGAAATTGCAGTTATTGACCAAGAAAC
CACTTTATCTTCATCTGCATCAAACTTTGCACAAGGAA

Alignment

ORF - retro_btau_573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEVTRSLLQRWGASFRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATCL
          MSEVTRSLL.RWGASFRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIAT.L
Retrocopy MSEVTRSLLLRWGASFRRGADFDSWGQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKKTIGKIATRL

Parental  ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGEEENLEFEEDEEEGGA
          ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPG.EENLEFEEDE.EGGA
Retrocopy ELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKEFPFDVQPVPLRRILAPGGEENLEFEEDE*EGGA

Parental  GAGSPDSFPARVPGTLLPRLPSEPGMTLLTIKIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVA
          GAGSPDSFPARVP.TLLPRLPSEPGM.LLTIKIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVA
Retrocopy GAGSPDSFPARVPDTLLPRLPSEPGMMLLTIKIEKIGLKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVA

Parental  SRKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT
          SRKEDTYVHFNVDIELQKHVEKLTKGAA...EFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT
Retrocopy SRKEDTYVHFNVDIELQKHVEKLTKGAAXXXEFKHYKPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPT

Parental  DFKRKKLQLLTKKPLYLHLHQTLHKE
          DFKRKKLQLLTKKPLYLHLHQTLHKE
Retrocopy DFKRKKLQLLTKKPLYLHLHQTLHKE

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	0.14 RPM	7.35 RPM
ERP005899_muscle	0.11 RPM	16.79 RPM
SRP017611_brain	0.41 RPM	10.92 RPM
SRP017611_kidney	0.06 RPM	16.06 RPM
SRP017611_liver	0.00 RPM	7.55 RPM
SRP030211_testis	0.15 RPM	13.69 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_573 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_573 has 0 orthologous retrocopies within eutheria group .

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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,