RetrogeneDB ID: retro_btau_310

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:116197013..116197376(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000033740
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.89449
• Ensembl ID: ENSBTAG00000021680
• Aliases: SKA2, FAM33A
• Description: spindle and kinetochore-associated protein 2 [Source:RefSeq peptide;Acc:NP_001033668]

Sequence

>retro_btau_310
ATGGAGGCGGAGGTCGATAAGCTGGAACTGATGTTCCAGAAAGCTGACTCTGATCTGGACTACATTCAGTACAGGCTGGA
ATATGAAATCAAGACTAATTATCCTGATTCAGCAGGCAAGAAAAATCCAGTTACACTTTTAAAGGAATTGTCAGCAATAA
AGTCTCGATATCAAACTTTGCATGTTCGCTTTAAACCAACTGCTGTGGAGCAGAAAGAGACTAAGAGCCGCATTTGTGCT
ACTTTCAATAAGACTCTGACCTTGATACAAGAACTGCAGAAGGAAACAGACCTGGAGTTGTTACCACTGACTGAAGAAGA
GAAAACTGCGGCAGAGCAATTAAGAGCTCACATGTCAGACTTA

Alignment

ORF - retro_btau_310 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAEVDKLELMFQKADSDLDYIQYRLEYEIKTNYPDSAGKKNPVTLLKELSAIKSRYQTLHVRFKPIAVE
          MEAEVDKLELMFQKADSDLDYIQYRLEYEIKTNYPDSAGKKNPVTLLKELSAIKSRYQTLHVRFKP.AVE
Retrocopy MEAEVDKLELMFQKADSDLDYIQYRLEYEIKTNYPDSAGKKNPVTLLKELSAIKSRYQTLHVRFKPTAVE

Parental  QKETKSRICATFNKTMTLIQELQKETDLELLPLTEEEKTAAEQLRAHMSDL
          QKETKSRICATFNKT.TLIQELQKETDLELLPLTEEEKTAAEQLRAHMSDL
Retrocopy QKETKSRICATFNKTLTLIQELQKETDLELLPLTEEEKTAAEQLRAHMSDL

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	7.21 RPM
ERP005899_muscle	0.00 RPM	8.39 RPM
SRP017611_brain	0.05 RPM	14.30 RPM
SRP017611_kidney	0.06 RPM	11.38 RPM
SRP017611_liver	0.00 RPM	2.64 RPM
SRP030211_testis	0.05 RPM	24.66 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_310 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_310 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021680	2 retrocopies	retro_btau_310 , retro_btau_945,
Canis familiaris	ENSCAFG00000029233	1 retrocopy	retro_cfam_766,
Cavia porcellus	ENSCPOG00000006051	1 retrocopy	retro_cpor_542,
Dipodomys ordii	ENSDORG00000010768	2 retrocopies	retro_dord_103, retro_dord_281,
Equus caballus	ENSECAG00000015007	1 retrocopy	retro_ecab_987,
Felis catus	ENSFCAG00000022802	1 retrocopy	retro_fcat_1111,
Homo sapiens	ENSG00000182628	1 retrocopy	retro_hsap_4214,
Loxodonta africana	ENSLAFG00000003405	1 retrocopy	retro_lafr_1215,
Myotis lucifugus	ENSMLUG00000010942	1 retrocopy	retro_mluc_83,
Monodelphis domestica	ENSMODG00000014619	1 retrocopy	retro_mdom_347,
Mustela putorius furo	ENSMPUG00000015241	1 retrocopy	retro_mputfur_1435,
Mus musculus	ENSMUSG00000020492	2 retrocopies	retro_mmus_370, retro_mmus_778,
Otolemur garnettii	ENSOGAG00000026072	4 retrocopies	retro_ogar_1882, retro_ogar_2937, retro_ogar_3032, retro_ogar_907,
Rattus norvegicus	ENSRNOG00000025981	3 retrocopies	retro_rnor_1606, retro_rnor_523, retro_rnor_733,
Sorex araneus	ENSSARG00000011128	2 retrocopies	retro_sara_60, retro_sara_662,
Ictidomys tridecemlineatus	ENSSTOG00000024169	4 retrocopies	retro_itri_1115, retro_itri_1275, retro_itri_1434, retro_itri_725,
Tarsius syrichta	ENSTSYG00000006158	3 retrocopies	retro_tsyr_1620, retro_tsyr_2034, retro_tsyr_748,
Tursiops truncatus	ENSTTRG00000017196	1 retrocopy	retro_ttru_143,