RetrogeneDB ID: retro_btau_1501

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:84904096..84904703(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSBTAG00000019494
• Aliases: None
• Description: 60S ribosomal protein L10a [Source:UniProtKB/Swiss-Prot;Acc:Q5E9E6]

Sequence

>retro_btau_1501
ATGAGCAGTGAAGTCTTCTGTGACACCCTGTATGAGACAGTGCAGGAAGTCCTGCATGGGAATCAACACAAGTGCCAAAA
TGTTCTGGAAATGGTGGATCTTCAGATCAGCCTGAAGAACTGTGACCTCAGAAGGACAAACACTTCTCAGCACTGTCAGG
CTTAAGTTCATTCCCCTTACCAAGTTCTCCATATATGTTCTGGGAGACCAGCAGCACTGTGATGAGGTAAGGCTGTGGAT
AAATCTCCCATATGAACATCAAGGCACTGAAGAAAATAACAATAGAAAACGGGTCAAGAAGCTAGCCAACAAGTATGACT
TTTTGGCTCCAGAATCTCTGTTTAAGCAGGTCCCATAAATCCTGGGCCCACGCCTGAATAACATTGGCAAACTCCCTTCC
TTGCTGACCCACAATGAGAACATGATGGCCAAAGTTGATGACGTAAAGTCCATGATCAAGTTTCAGATAAAGAAGATGCT
GTGTCTGTCAGTGGCTGTTGGCCATGTGAAGATGATGGATGATGAGCTTGTGTACAACATCCACTTAGCTGTTAAACTTC
TGGTGTCATTGCACAAGAAAAACTAGCAGAATGTCCAGTCTGTACAT

Alignment

ORF - retro_btau_1501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.83 %
• Parental protein coverage: 94.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYD-PQKDKRFS-GTVRLKSTPRPKFSVCVL
          MSS.V..DTLYE.V.EVLHGNQ.K....LE.V.LQISLKN.D.PQKDK.FS..TVRLK..P..KFS..VL
Retrocopy MSSEVFCDTLYETVQEVLHGNQHKCQNVLEMVDLQISLKNCD<PQKDKHFS<STVRLKFIPLTKFSIYVL

Parental  GDQQHCDEAKA-VDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSL
          GDQQHCDE.......P..........N..K..VKKLA.KYD.FLA.ESL.KQ.P.ILGP.LN..GK.PSL
Retrocopy GDQQHCDEVRLWINLPY-EHQGTEENNNRKR-VKKLANKYD-FLAPESLFKQVP*ILGPRLNNIGKLPSL

Parental  LTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALY
          LTHNENM.AKVD.VKS.IKFQ.KK.LCL.VAVGHVKM.DDELVYNIHLAV..LVSL.KKN.QNV....
Retrocopy LTHNENMMAKVDDVKSMIKFQIKKMLCLSVAVGHVKMMDDELVYNIHLAVKLLVSLHKKN*QNVQSVH

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	0.29 RPM	71.95 RPM
ERP005899_muscle	0.32 RPM	878.62 RPM
SRP017611_brain	0.18 RPM	58.88 RPM
SRP017611_kidney	0.30 RPM	153.22 RPM
SRP017611_liver	0.38 RPM	130.48 RPM
SRP030211_testis	0.25 RPM	62.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1501 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1501 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019494	4 retrocopies	retro_btau_138, retro_btau_1501 , retro_btau_1634, retro_btau_87,
Dasypus novemcinctus	ENSDNOG00000012921	3 retrocopies	retro_dnov_157, retro_dnov_1917, retro_dnov_469,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Mus musculus	ENSMUSG00000037805	8 retrocopies	retro_mmus_1110, retro_mmus_1304, retro_mmus_1422, retro_mmus_149, retro_mmus_1737, retro_mmus_2038, retro_mmus_2652, retro_mmus_452,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Sus scrofa	ENSSSCG00000001543	7 retrocopies	retro_sscr_1169, retro_sscr_1174, retro_sscr_120, retro_sscr_246, retro_sscr_379, retro_sscr_461, retro_sscr_465,