RetrogeneDB ID: retro_btau_766

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:47352256..47352698(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDFIP1
• Ensembl ID: ENSBTAG00000047747
• Aliases: None
• Description: None

Sequence

>retro_btau_766
ACAACACTACCCAGTTATGATGAAGGCAAGAGAATCAAGCATGAAACTACTATCCCTTCAGTTTCTGGAAGAGATGAGTA
TTTTGTGGGTCAGGATGACTTCGATAATGCTGACCAACTTAGTTTAGGCAACAACAGGATTTTCATGTGAACTTTTTTAT
GGCATTCTTTAAAACTAGATTGGGTATTTCCTGTCTGCTTTCCTGGCCACTTCAACTGCAGGAAAGTATGAGGCCATTTC
AGGATTTGGCCTCTCTCTAATCAAGCAGATCCTTGTTGTCAGGTTTTCCACCTATTTCCCTGGATATTTTGATGGTCAGA
ATTGTCTCTGGTGGGTGTTTCTGGTTTTAGGTTTTCTCCTGTTTCTCAGAGGATTTGTTAATTATGCAAAAGTTTGGAAG
ATATAAAAACTCAAATTACTGCAGGACAGAGTTCTCTTTATT

Alignment

ORF - retro_btau_766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.08 %
• Parental protein coverage: 70.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TTLPSYDEAERTKAEATIPLVPGRDEEFAGREEFDDPDQMRIGNDGIFMLTF-FMAF-LFNWIGFFLSFC
          TTLPSYDE..R.K.E.TIP.V.GRDE.F.G...FD..DQ...GN..IFM.TF.FMAF.L.N.IG.FLS..
Retrocopy TTLPSYDEGKRIKHETTIPSVSGRDEYFVGQDDFDNADQLSLGNNRIFM*TF<FMAF<L*N*IGYFLSAF

Parental  LTTSAAGRYGAISGFGLSLIKWILIVRFSTYFPGYFDGQYWLWWVFLVLGFLLFLRGFINYAKVRKMPEN
          L.TS.AG.Y.AISGFGLSLIK.IL.VRFSTYFPGYFDGQ..LWWVFLVLGFLLFLRGF.NYAKV.K....
Retrocopy LATSTAGKYEAISGFGLSLIKQILVVRFSTYFPGYFDGQNCLWWVFLVLGFLLFLRGFVNYAKVWKI*K-

Parental  FSNLPRTRVLFI
          ...L...RVLFI
Retrocopy -LKLLQDRVLFI

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	109.08 RPM
ERP005899_muscle	0.00 RPM	59.60 RPM
SRP017611_brain	0.00 RPM	310.35 RPM
SRP017611_kidney	0.00 RPM	193.23 RPM
SRP017611_liver	0.00 RPM	34.66 RPM
SRP030211_testis	0.03 RPM	29.85 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_766 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_766 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047747	1 retrocopy	retro_btau_766 ,
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175,
Equus caballus	ENSECAG00000021907	1 retrocopy	retro_ecab_261,
Homo sapiens	ENSG00000131507	1 retrocopy	retro_hsap_1091,
Gorilla gorilla	ENSGGOG00000004879	1 retrocopy	retro_ggor_859,
Macaca mulatta	ENSMMUG00000016787	1 retrocopy	retro_mmul_846,
Pongo abelii	ENSPPYG00000015896	1 retrocopy	retro_pabe_908,
Pan troglodytes	ENSPTRG00000017358	1 retrocopy	retro_ptro_743,
Sarcophilus harrisii	ENSSHAG00000002466	1 retrocopy	retro_shar_738,
Sus scrofa	ENSSSCG00000025295	1 retrocopy	retro_sscr_301,
Ictidomys tridecemlineatus	ENSSTOG00000005153	1 retrocopy	retro_itri_1454,