RetrogeneDB ID: retro_btau_575

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:24596939..24597447(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAPTM4A
• Ensembl ID: ENSBTAG00000020894
• Aliases: None
• Description: Lysosomal-associated transmembrane protein 4A [Source:UniProtKB/Swiss-Prot;Acc:Q6QRN8]

Sequence

>retro_btau_575
TATGAAGTCATTGGCAATTACTGTTCGTCCCGGAGAATGACTGATAATGCCTGTGTTCTTTTTTGCTGTCTCTGTTCTTA
ATGTTTACAATCAGTTTAATGCTGGTATACGGAGGAATTTCTTATCAATTGGGTTGGTTGATTCTGCTCGTCTGCTCCTG
GCTTTTTGACTTCTTTCTCAGCTGCCTGGTTGCTTTCAGTTCTCTCACTTATTTGCCAAGAATCAAAGACTATATGGATC
AATTACCTGATTTTCCCTATAAAGGTGACCTCCTGGCATCAGACTCCAGCTACCTCCTGTTCATTGTTCTTGTGTTCTTC
GCCTTGTTCATCACTTTAAGGCTTATCTGATCAACTGTGTTTGGGACTGTTATGAATACATCAGCAGCAACATGCTATAG
ATTGCTGTGTATCCGGCCTTTGAAGCACCTCCCCAGTATGTTTTGCCAACCTATGAAATGGCAGTGAAGATGCCTGGGAA
AGAACCAACGCCTCCTTATATACCTGCC

Alignment

ORF - retro_btau_575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 72.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YEVIGNYYSSERMADNACVLF-AVSVL-MFIISSMLVYGAISYQVGWLIPFFCYRLFDFVLSCLVAISSL
          YEVIGNY.SS.RM.DNACVLF.AVSVL.MF.IS.MLVYG.ISYQ.GWLI...C..LFDF.LSCLVA.SSL
Retrocopy YEVIGNYCSSRRMTDNACVLF>AVSVL>MFTISLMLVYGGISYQLGWLILLVCSWLFDFFLSCLVAFSSL

Parental  TYLPRIKEYLDQLPDFPYKDDLLALDSSCLLFIVLVFFALFII-FKAYLINCVWNCYKYINNRNMPEIAV
          TYLPRIK.Y.DQLPDFPYK.DLLA.DSS.LLFIVLVFFALFI..FKAYLINCVW.CY.YI...NM..IAV
Retrocopy TYLPRIKDYMDQLPDFPYKGDLLASDSSYLLFIVLVFFALFIT<FKAYLINCVWDCYEYISS-NML*IAV

Parental  YPAFEAPPQYVLPTYEMAVKMPEKEPPPPYIPA
          YPAFEAPPQYVLPTYEMAVKMP.KEP.PPYIPA
Retrocopy YPAFEAPPQYVLPTYEMAVKMPGKEPTPPYIPA

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	129.63 RPM
ERP005899_muscle	0.00 RPM	101.83 RPM
SRP017611_brain	0.00 RPM	85.24 RPM
SRP017611_kidney	0.00 RPM	248.59 RPM
SRP017611_liver	0.00 RPM	110.54 RPM
SRP030211_testis	0.00 RPM	230.55 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_575 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_575 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Bos taurus	ENSBTAG00000020894	1 retrocopy	retro_btau_575 ,
Choloepus hoffmanni	ENSCHOG00000011200	2 retrocopies	retro_chof_1916, retro_chof_2320,
Callithrix jacchus	ENSCJAG00000007433	1 retrocopy	retro_cjac_839,
Echinops telfairi	ENSETEG00000002569	1 retrocopy	retro_etel_591,
Mustela putorius furo	ENSMPUG00000013714	1 retrocopy	retro_mputfur_657,
Ochotona princeps	ENSOPRG00000012401	2 retrocopies	retro_opri_356, retro_opri_474,
Pteropus vampyrus	ENSPVAG00000002909	3 retrocopies	retro_pvam_779, retro_pvam_847, retro_pvam_873,