RetrogeneDB ID: retro_btau_1284

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:73263282..73263914(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000005099
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSBTAG00000009908
• Aliases: RPS3A, RPS3AE
• Description: 40S ribosomal protein S3a [Source:UniProtKB/Swiss-Prot;Acc:Q56JV9]

Sequence

>retro_btau_1284
ATGGCGATCGACAAGAACAAGCGCCTTACGAAAGGAGGCAAAAAGGGAGCCAAAAAGAAAGTGGTTGACCCATTTTCTAA
AAAAGACTGGTATGATGTGAAAGCACCAGCTATGTTCAATATAAGGAATATTGGGAAAACATTGGTTACGAGAACTCAAG
GAACCAAAATCGCATCTGATGGCCTCAAAGGTCGTGTTTTTGAAGTGAGTCTTGCTGATCTGCAGAATGGTGAAGTAGCA
TTTAGAAAATTCAAGCTAATTACTGAGGATGTTCAGGGCAAAACCTGCCTAATTTTCATGGTATGGATCTTATCCCGTGA
CAAAATGTGCTCCATGGTCAAAAAATGGCAGACCATGATTGAAGCCCACGTTGATGTCAAGACGACCGATGGTTACTTGC
TTCGTCTGTTCTGTGTGGGTTTTACTAAAAAGCGCGACAGTCAGATTCGGAAGACCTCTTACGCCCAGCACCAGCAGGTG
CACCAGATGATGGAAATCATGACCCCAGAGGTGCAGACAATGATTTGAAAGAGGTGGTCAATAAATTGATTCCAGATAGC
ATTGGAAAAGACATAGAAAAGGCTTGCCAATCTATTTATCCACTCCATGATGTCTTCGTTAGAAATGCTGAA

Alignment

ORF - retro_btau_1284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.4 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
          MA..KNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
Retrocopy MAIDKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS

Parental  LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
          LADLQN.EVAFRKFKLITEDVQGK.CL..F....L.RDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
Retrocopy LADLQNGEVAFRKFKLITEDVQGKTCLI-FMVWILSRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV

Parental  GFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQT-NDLKEVVNKLIPDSIGKDIEKACQSIYPLHD
          GFTKKR..QIRKTSYAQHQQV.Q....MMEIMT.EVQT.NDLKEVVNKLIPDSIGKDIEKACQSIYPLHD
Retrocopy GFTKKRDSQIRKTSYAQHQQVHQ----MMEIMTPEVQT<NDLKEVVNKLIPDSIGKDIEKACQSIYPLHD

Parental  VFVRKVK
          VFVR...
Retrocopy VFVRNAE

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	0.22 RPM	323.49 RPM
ERP005899_muscle	0.05 RPM	1737.76 RPM
SRP017611_brain	0.09 RPM	176.23 RPM
SRP017611_kidney	0.18 RPM	547.73 RPM
SRP017611_liver	0.15 RPM	185.00 RPM
SRP030211_testis	0.02 RPM	302.76 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1284 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1284 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018425	11 retrocopies	retro_amel_1333, retro_amel_1361, retro_amel_1380, retro_amel_1514, retro_amel_159, retro_amel_1697, retro_amel_1732, retro_amel_1739, retro_amel_230, retro_amel_367, retro_amel_863,
Bos taurus	ENSBTAG00000009908	3 retrocopies	retro_btau_1284 , retro_btau_1733, retro_btau_233,
Canis familiaris	ENSCAFG00000007990	7 retrocopies	retro_cfam_103, retro_cfam_146, retro_cfam_169, retro_cfam_170, retro_cfam_179, retro_cfam_222, retro_cfam_77,
Callithrix jacchus	ENSCJAG00000002268	7 retrocopies	retro_cjac_2, retro_cjac_21, retro_cjac_249, retro_cjac_312, retro_cjac_337, retro_cjac_368, retro_cjac_78,
Dipodomys ordii	ENSDORG00000002250	10 retrocopies	retro_dord_142, retro_dord_168, retro_dord_193, retro_dord_209, retro_dord_229, retro_dord_314, retro_dord_380, retro_dord_752, retro_dord_757, retro_dord_95,
Erinaceus europaeus	ENSEEUG00000004994	4 retrocopies	retro_eeur_297, retro_eeur_510, retro_eeur_517, retro_eeur_66,
Gorilla gorilla	ENSGGOG00000003182	2 retrocopies	retro_ggor_70, retro_ggor_97,
Microcebus murinus	ENSMICG00000004921	9 retrocopies	retro_mmur_1230, retro_mmur_1289, retro_mmur_193, retro_mmur_299, retro_mmur_330, retro_mmur_526, retro_mmur_592, retro_mmur_626, retro_mmur_945,
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Oryctolagus cuniculus	ENSOCUG00000007011	1 retrocopy	retro_ocun_257,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,
Vicugna pacos	ENSVPAG00000004235	8 retrocopies	retro_vpac_253, retro_vpac_31, retro_vpac_322, retro_vpac_439, retro_vpac_486, retro_vpac_497, retro_vpac_529, retro_vpac_88,