RetrogeneDB ID: retro_btau_1190

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:18522323..18522888(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000009268
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAL1
• Ensembl ID: ENSBTAG00000015930
• Aliases: None
• Description: Dynein light chain 1, axonemal [Source:UniProtKB/Swiss-Prot;Acc:Q2KID4]

Sequence

>retro_btau_1190
ATGGCAGAAGCAACAACAATCAAAGGAGCACTAGCCAGAGGGGAAGAGAAAACCGGCCAGAAGCCATCTGAAGCCAGAGC
GATAAGGCTGTATGCCCAGATTCCCCCTGTAGAGAAGATGGACGCATCATTGTCCACACTTTCTAACTGTGAGAAGCTTT
CACTGACTACAAACTGCATTGAAAAAACTGCAAACCTGAATGACTTAAAAACCTTAAGAATATTGTCTTTAGGAAGAAAC
AACACAAACAACTTAAATGAACTGGAAGTAGTAGGGGACACATTAGAAGAACTGTGGATCCCCTACAATTTTACTGAGAA
GTTGAAAGGGACCCATGTAATGAAGAAACTGAAGATTCTCTACATGTCTAATAACCTGGTGAAAGATGGCTGAATTTGTG
AAGCTGGCAGAACTGCCATGCCTAGAAGACCTGGTGTTTGTAGGCAATCTCTTGGAAGAGAAACATTCTGCTGAGAACTG
GATTGAAGAGGCAACCAAGACAATGCCCAAACTGAAAAAGCTAGATGGTACCCCAGTAGTTAAAGAAGATGAGGAAGAAG
ATAAC

Alignment

ORF - retro_btau_1190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKATTIKEALARWEEKTSQKPSEAREIKLYAQIPPIEKMDASLSTLSNCEKLSLSTNCIEKIANLNGLK
          MA.ATTIK.ALAR.EEKT.QKPSEAR.I.LYAQIPP.EKMDASLSTLSNCEKLSL.TNCIEK.ANLN.LK
Retrocopy MAEATTIKGALARGEEKTGQKPSEARAIRLYAQIPPVEKMDASLSTLSNCEKLSLTTNCIEKTANLNDLK

Parental  NLRILSLGRNNIKNLNGLEAVGDTLEELWISYNFIEKLKGIHVMKKLKILYMSNNLVKD-W-AEFVKLAE
          .LRILSLGRNN..NLN.LE.VGDTLEELWI.YNF.EKLKG.HVMKKLKILYMSNNLVKD.W.AEFVKLAE
Retrocopy TLRILSLGRNNTNNLNELEVVGDTLEELWIPYNFTEKLKGTHVMKKLKILYMSNNLVKD<W<AEFVKLAE

Parental  LPCLEDLVFVGNPLEEKHSAEGNWVEEATKRVPKLKKLDGTPVIKEDEEEDN
          LPCLEDLVFVGN.LEEKHSAE.NW.EEATK..PKLKKLDGTPV.KEDEEEDN
Retrocopy LPCLEDLVFVGNLLEEKHSAE-NWIEEATKTMPKLKKLDGTPVVKEDEEEDN

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	2.23 RPM
ERP005899_muscle	0.00 RPM	1.48 RPM
SRP017611_brain	0.00 RPM	13.70 RPM
SRP017611_kidney	0.00 RPM	12.33 RPM
SRP017611_liver	0.00 RPM	1.96 RPM
SRP030211_testis	0.00 RPM	12.75 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1190 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1190 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015930	1 retrocopy	retro_btau_1190 ,
Cavia porcellus	ENSCPOG00000010655	1 retrocopy	retro_cpor_25,
Drosophila melanogaster	FBgn0033408	1 retrocopy	retro_dmel_26,