RetrogeneDB ID: retro_btau_411

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:61716756..61717257(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000023318
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS24
• Ensembl ID: ENSBTAG00000007398
• Aliases: None
• Description: 28S ribosomal protein S24, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q2M2T7]

Sequence

>retro_btau_411
ATGGTGGCGCTCTACTGCGGTGGCGGGCTCAGGCCTCTGATGCTGTCCTGGAGCCGGGATCTGCCCTGCATCTGGCACGC
CCTGCATACCTCCGTGGTTTGCTTCAAGAACCGGGTGGCCCGAGTCCGAGTGGACAAGGGGAACAAACCAGTGACCTACG
AGGAAGCGCATGCGCCTCACTACATCGCCCACCGCAAGGGCTGGCTGTCACTGCATACAGGTAACCTGGATGGGGAGGAC
CACGCTGCCGAGCTAACAGTGGAAGATGTTTTCCTTCGCAAATTTATGCTGGGCACCTTCCCAGGCTGCCTGGCTGACCA
GCTTATTCTGAAGCGCTGGGCTAATCAGGTGGAGATCTGTGCCCTGGTCCTGAGGCAGCTACCTGCACACAAGTTCTACT
TCCTTGTGGGCTACAGTGAGACCCTGCTGTCCCACTTTTACAAGTGTCCTGTTCGTCTGCACCTCCAAACTGTTCCCTCA
AAGGTTGTGTATAAGTATATG

Alignment

ORF - retro_btau_411 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVALYCGGGLRPLMLSWSRDLPCIWRALHTSAVCFKNRAARVRVGKGNKPVTYEEAHAPHYIAHRKGWLS
          MVALYCGGGLRPLMLSWSRDLPCIW.ALHTS.VCFKNR.ARVRV.KGNKPVTYEEAHAPHYIAHRKGWLS
Retrocopy MVALYCGGGLRPLMLSWSRDLPCIWHALHTSVVCFKNRVARVRVDKGNKPVTYEEAHAPHYIAHRKGWLS

Parental  LHTGNLDGEDHAAERTVEDVFLRKFMLGTFPGCLADQLILKRRANQVEICALVLRQLPAHKFYFLVGYSE
          LHTGNLDGEDHAAE.TVEDVFLRKFMLGTFPGCLADQLILKR.ANQVEICALVLRQLPAHKFYFLVGYSE
Retrocopy LHTGNLDGEDHAAELTVEDVFLRKFMLGTFPGCLADQLILKRWANQVEICALVLRQLPAHKFYFLVGYSE

Parental  TLLSHFYKCPVRLHLQTVPSKVVYKYI
          TLLSHFYKCPVRLHLQTVPSKVVYKY.
Retrocopy TLLSHFYKCPVRLHLQTVPSKVVYKYM

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	4.33 RPM
ERP005899_muscle	0.05 RPM	12.41 RPM
SRP017611_brain	0.05 RPM	7.49 RPM
SRP017611_kidney	0.30 RPM	11.91 RPM
SRP017611_liver	0.08 RPM	4.98 RPM
SRP030211_testis	0.18 RPM	21.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_411 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_411 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017491	1 retrocopy	retro_amel_1126,
Bos taurus	ENSBTAG00000007398	1 retrocopy	retro_btau_411 ,
Choloepus hoffmanni	ENSCHOG00000003106	1 retrocopy	retro_chof_2334,
Dasypus novemcinctus	ENSDNOG00000016853	3 retrocopies	retro_dnov_1195, retro_dnov_153, retro_dnov_2049,
Echinops telfairi	ENSETEG00000016782	1 retrocopy	retro_etel_1350,
Homo sapiens	ENSG00000062582	1 retrocopy	retro_hsap_836,
Gorilla gorilla	ENSGGOG00000005692	1 retrocopy	retro_ggor_687,
Loxodonta africana	ENSLAFG00000011905	1 retrocopy	retro_lafr_426,
Macaca mulatta	ENSMMUG00000002405	1 retrocopy	retro_mmul_1089,
Monodelphis domestica	ENSMODG00000013889	1 retrocopy	retro_mdom_1785,
Pan troglodytes	ENSPTRG00000019127	1 retrocopy	retro_ptro_583,
Pteropus vampyrus	ENSPVAG00000015911	4 retrocopies	retro_pvam_1129, retro_pvam_1360, retro_pvam_180, retro_pvam_978,
Tursiops truncatus	ENSTTRG00000002938	1 retrocopy	retro_ttru_1860,