RetrogeneDB ID: retro_btau_440

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:47717012..47717333(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000017953
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS27A
• Ensembl ID: ENSBTAG00000015473
• Aliases: None
• Description: Ubiquitin-40S ribosomal protein S27a Ubiquitin 40S ribosomal protein S27a [Source:UniProtKB/Swiss-Prot;Acc:P62992]

Sequence

>retro_btau_440
CAGCAACTGGAAGACGGATTTCCTTTGTCTAACTACAACATTCAAAAGGAGTCCACTCTTCATCTTGTGCTGAGACGTTG
TGGTGGAGCTAAGAGAAGGAAGAAGTCTCATGCCACTCCCAAGAAGAACAAGCATAAGAGAAAAAAGGTTAAGCTGGCTG
TCCTGAAAAACTACAAGGTGGAGGAGAATGGCAGAATCAATTACCTTCACTGGGAGTGTCCTTCAGATGAATAATGTGCT
GAAGTTTTTATGACCAGTCACTTTGACAGACATTATTATGGCAAATGTTGTCTGACCTATTTCAACAAACCAGAAGACAA
G

Alignment

ORF - retro_btau_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.9 %
• Parental protein coverage: 69.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQLEDGRTLSDYNIQKESTLHLVLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRL
          .QLEDG..LS.YNIQKESTLHLVLR..GGAK.RKK.S..TPKKNKHKRKKVKLAVLK.YKV.ENG.I..L
Retrocopy QQLEDGFPLSNYNIQKESTLHLVLRRCGGAKRRKK-SHATPKKNKHKRKKVKLAVLKNYKVEENGRINYL

Parental  RRECPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPEDK
          ..ECPSDE..A.VFM.SHFDRHY.GKCCLTY.FNKPEDK
Retrocopy HWECPSDE*CAEVFMTSHFDRHYYGKCCLTY-FNKPEDK

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	163.66 RPM
ERP005899_muscle	0.00 RPM	850.43 RPM
SRP017611_brain	0.05 RPM	94.92 RPM
SRP017611_kidney	0.00 RPM	263.88 RPM
SRP017611_liver	0.00 RPM	151.02 RPM
SRP030211_testis	0.00 RPM	155.57 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_440 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Bos taurus	ENSBTAG00000015473	6 retrocopies	retro_btau_1115, retro_btau_1213, retro_btau_1631, retro_btau_395, retro_btau_440 , retro_btau_664,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Gorilla gorilla	ENSGGOG00000007678	9 retrocopies	retro_ggor_1290, retro_ggor_1291, retro_ggor_1502, retro_ggor_1749, retro_ggor_179, retro_ggor_203, retro_ggor_2373, retro_ggor_2858, retro_ggor_2885,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Pan troglodytes	ENSPTRG00000011928	1 retrocopy	retro_ptro_32,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Ictidomys tridecemlineatus	ENSSTOG00000009566	5 retrocopies	retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,