RetrogeneDB ID: retro_btau_1701

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:42546055..42546652(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000010148
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAGLN2
• Ensembl ID: ENSBTAG00000002068
• Aliases: None
• Description: Transgelin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5E9F5]

Sequence

>retro_btau_1701
ATGGCCAACAGGGGACCTGCGTATGGCCTGAGCCAGGAGGTACAGCAGAAGATTGATAAACAATACGATGCAGACCTGGA
GCAAATCCTGATCCAGTGGATCACCACCCAGTGCCGCAAGCATGTGAGCCGGCCTCAGCCTGGGTGCACGAACTTCCAGA
ACTGGCTCAAGGATGGCACGGTGCTGTGTGAGCTCATTAATGGACTGTACCCCGAGGGGCAGGCCCCAGTGAAGAAGATC
CAGGCCTCCACCACAGCCTTCAAGCAGATGGGGCAGATCTCCCAGTTCCTGCAAGCAGCCGAGCGCTACGGCATCAACAC
CAATGACATCTCCCAGACTGTGGACCTCTGGGAAGGAAAGAATATGGCCTGTGTGCAGCGGACACTGATGAATCTGGGCA
GGCTAGTGGTAGCATGGGACGATGGGCTCTTCTCTGGGGATCCTAACTGGTTTACCAAGAAATCCAAGGAGAACCCTCGG
TACTTCCCGGACAACCAACTGCAGGAGGGCAAGAATTTGTTTGGCTTACAGATGGGGACCAACCACGGGGCTTCTCAGGC
AGGCTTGACTGACTATGCGATGCCATGCCAGATCCTC

Alignment

ORF - retro_btau_1701 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANRGPAYGLSREVQQKIEKQYDADLEQILIQWITTQCRKDVGRPQPGRENFQNWLKDGTVLCELINGLY
          MANRGPAYGLS.EVQQKI.KQYDADLEQILIQWITTQCRK.V.RPQPG..NFQNWLKDGTVLCELINGLY
Retrocopy MANRGPAYGLSQEVQQKIDKQYDADLEQILIQWITTQCRKHVSRPQPGCTNFQNWLKDGTVLCELINGLY

Parental  PEGQAPVKKIQASTMAFKQMEQISQFLQAAERYGINTTDIFQTVDLWEGKNMACVQRTLMNLGGLAVARD
          PEGQAPVKKIQAST.AFKQM.QISQFLQAAERYGINT.DI.QTVDLWEGKNMACVQRTLMNLG.L.VA.D
Retrocopy PEGQAPVKKIQASTTAFKQMGQISQFLQAAERYGINTNDISQTVDLWEGKNMACVQRTLMNLGRLVVAWD

Parental  DGLFSGDPNWFPKKSKENPRYFSDNQLQEGKNVIGLQMGTNRGASQAGMTGYGMPRQIL
          DGLFSGDPNWF.KKSKENPRYF.DNQLQEGKN..GLQMGTN.GASQAG.T.Y.MP.QIL
Retrocopy DGLFSGDPNWFTKKSKENPRYFPDNQLQEGKNLFGLQMGTNHGASQAGLTDYAMPCQIL

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	36.84 RPM
ERP005899_muscle	0.00 RPM	183.60 RPM
SRP017611_brain	0.05 RPM	29.78 RPM
SRP017611_kidney	0.06 RPM	225.05 RPM
SRP017611_liver	0.00 RPM	81.70 RPM
SRP030211_testis	0.03 RPM	61.43 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1701 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1701 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701 ,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Bos taurus	ENSBTAG00000020764	1 retrocopy	retro_btau_612,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Homo sapiens	ENSG00000158710	1 retrocopy	retro_hsap_4108,
Macropus eugenii	ENSMEUG00000006573	9 retrocopies	retro_meug_1092, retro_meug_1242, retro_meug_128, retro_meug_1442, retro_meug_1998, retro_meug_309, retro_meug_483, retro_meug_690, retro_meug_880,
Myotis lucifugus	ENSMLUG00000026228	1 retrocopy	retro_mluc_274,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Monodelphis domestica	ENSMODG00000010032	1 retrocopy	retro_mdom_1178,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Pongo abelii	ENSPPYG00000000648	2 retrocopies	retro_pabe_3310, retro_pabe_3364,
Pan troglodytes	ENSPTRG00000001533	1 retrocopy	retro_ptro_2788,
Sus scrofa	ENSSSCG00000006395	2 retrocopies	retro_sscr_312, retro_sscr_313,
Tarsius syrichta	ENSTSYG00000001645	2 retrocopies	retro_tsyr_1911, retro_tsyr_950,
Tursiops truncatus	ENSTTRG00000001814	1 retrocopy	retro_ttru_1614,