RetrogeneDB ID: retro_btau_1541

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:68122643..68123270(+)
• Located in intron of: ENSBTAG00000019457

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGC159500
• Ensembl ID: ENSBTAG00000021620
• Aliases: PITHD1, C2H1orf128
• Description: PITH domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001092360]

Sequence

>retro_btau_1541
CTTTCGCATGGCCATAGTGGGGACGGCTGCTGCTGCGCCGCCAAACGGGAGGAGCCTCCCTAGCAGCGCGGCCTGACCTT
CGGCCTGTACCTGCTCTTTGACCTGGAGCAGTCTCAGTGCCTCAAGGAGAGCCATGAGGGCAGCGGCCCTGGCGTCTTTA
GGCCATGGGAGGAGCTGACTGACCGCTCCAAGTTTGTTGAAAGTGATGCAGATGAAGAGCTTATGTTAAATATTCCATGT
ACTGGCAATGTCAAGCTCAAGGGCATCATTATAATGGGAGACAATGATGACTCACACCCCTCTGAGATGAGACTGTACAG
GAACATTCCACAGATGTCCTTTGATGATAGAGACAAGGAGCCAGATCAGACCTTTAGTCTGAACTGGGATCTTACAGGGG
AATTAGAGTATGCTACAGAAATTTCTCATTTTTCAAATATCTGTCATCTCTCAATTCATATTTCAAAAAAATTTGGAGCT
GATACCACAAAGGTCTTTTATATTGGCCTGAGAGGAGAATGGACTGAGCTTTGTTCACATGAGATGACCATCTACAATTA
TGAAGCATGAGCCAATCCAGCTGACCACAGGGTCCATCAGGTAACCCCACAGACACACTTTATTTCC

Alignment

ORF - retro_btau_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHGHSHGGGGCHCAAEREEPPEQRGLAYGLYLRIDLERLQCLNESREGSGRGVFKPWEERTDRSKFVES
          .SHGHS..G.GC.CAA.REEPP.QRGL..GLYL..DLE..QCL.ES.EGSG.GVF.PWEE.TDRSKFVES
Retrocopy LSHGHS--GDGCCCAAKREEPP*QRGLTFGLYLLFDLEQSQCLKESHEGSGPGVFRPWEELTDRSKFVES

Parental  DADEELLFNIPFTGNVKLKGIIIMGEDDDSHPSEMRLYKNIPQMSFDDTDREPDQTFSLNRDLTGELEYA
          DADEEL..NIP.TGNVKLKGIIIMG..DDSHPSEMRLY.NIPQMSFDD.D.EPDQTFSLN.DLTGELEYA
Retrocopy DADEELMLNIPCTGNVKLKGIIIMGDNDDSHPSEMRLYRNIPQMSFDDRDKEPDQTFSLNWDLTGELEYA

Parental  TKISRFSNVYHLSIHISKNFGADTTKVFYIGLRGEWTELRRHEVTICNYEASANPADHKVHQVTPQTHFI
          T.IS.FSN..HLSIHISK.FGADTTKVFYIGLRGEWTEL..HE.TI.NYEA.ANPADH.VHQVTPQTHFI
Retrocopy TEISHFSNICHLSIHISKKFGADTTKVFYIGLRGEWTELCSHEMTIYNYEA*ANPADHRVHQVTPQTHFI

Parental  S
          S
Retrocopy S

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	20.62 RPM
ERP005899_muscle	0.11 RPM	15.15 RPM
SRP017611_brain	0.05 RPM	56.09 RPM
SRP017611_kidney	0.06 RPM	22.11 RPM
SRP017611_liver	0.00 RPM	10.80 RPM
SRP030211_testis	0.07 RPM	52.02 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1541 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021620	2 retrocopies	retro_btau_1541 , retro_btau_939,
Tarsius syrichta	ENSTSYG00000007837	1 retrocopy	retro_tsyr_1726,