RetrogeneDB ID: retro_btau_211

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:28075089..28075890(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000023000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DFFA
• Ensembl ID: ENSBTAG00000013535
• Aliases: None
• Description: DNA fragmentation factor subunit alpha [Source:RefSeq peptide;Acc:NP_001068810]

Sequence

>retro_btau_211
ATGGAGGTGGCCAGCAGCCCTGCAGCTCCAGAACCCGGCGAGATCTGGGCTCTAAAGCAGTGTCTGCTGCGCTGCAACAA
CAGCCGCGAACAGCACGGCATGGCAGCCTCATGCCTCGAGGAGCTGAGGAACAAGGCTTCTGACATTCTGGCCATCGATA
AGTCCCAGGCGCCAGTCACCCTGGTCCTGGAAGAGGATGGCACCATAGTGGATGACTATGATTACTTCCTGTGTCTTCCT
GCCAATACTAAGTTTGTGGCATTGGCTGGGAATGAGAAGTGGACACACAATTCAGATGGAGGTACAGCTTGGATAACCCA
AGAGTCCTTCCACAGAGATGAAACAGACAGCGGGGCAGGGCTGAAGTGGAAGAACGTGGCCAGGCAGCTGAAGGAAGACC
TATCCAGCATCATCCTGATGTCCAAGGAGGAGCTCCAGATGCTCACTGATGACCCATGTTCGGAGCTGCCTCAGGAACTC
GGCCAAAATCATGTGGTAGTCCAGGGGCTCCAGAACACCCTCCAGCAGGTGCTTGACCAGAAAGAGGAAGCCCGTCAGTC
CAGACAGCTCGTGGAACTTTACCTCCAAGCTTTGGAGAAGGAAGGCAGCATCTTGTTGAAGCAGCAAGAGTCCAGAGCTG
ACCTCGGGGATGAAAGGGACGCTGCTGAGACGGGCGTTAGAAAGCGCTCCTCAGACATTATGCCTGCAAGCCAGATCCTC
TTAGTGCTAAAGGAGAAATCTGCCCCAGAGCTGAGTTTGTCTGGTCCGGATCTGGAAGTGGGCAAGCACCAGGGACCCTG
A

Alignment

ORF - retro_btau_211 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.33 %
• Parental protein coverage: 80.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVPGGPAAPEPGEIRALKQCLLRRNKSREQHGVAASCLKELRNKACDILAIDKSLAPVTLVLAEDGTIV
          MEV...PAAPEPGEI.ALKQCLLR.N.SREQHG.AASCL.ELRNKA.DILAIDKS.APVTLVL.EDGTIV
Retrocopy MEVASSPAAPEPGEIWALKQCLLRCNNSREQHGMAASCLEELRNKASDILAIDKSQAPVTLVLEEDGTIV

Parental  DDDDYFLCLPANTKFVVLAGNEKWTHNSDGGTAWITQESFDRDETDSGAGLKWKNVARQLKEDLSSIILL
          DD.DYFLCLPANTKFV.LAGNEKWTHNSDGGTAWITQESF.RDETDSGAGLKWKNVARQLKEDLSSIIL.
Retrocopy DDYDYFLCLPANTKFVALAGNEKWTHNSDGGTAWITQESFHRDETDSGAGLKWKNVARQLKEDLSSIILM

Parental  SEEELQMLIDVPCSELAQELSQSHVAVQGLQNTLQQVLDQREEARQSRQLLELYLRALEKEGGILSKQQE
          S.EELQML.D.PCSEL.QEL.Q.HV.VQGLQNTLQQVLDQ.EEARQSRQL.ELYL.ALEKEG.IL.KQQE
Retrocopy SKEELQMLTDDPCSELPQELGQNHVVVQGLQNTLQQVLDQKEEARQSRQLVELYLQALEKEGSILLKQQE

Parental  SRADLGDESDAVDTGIRESFSEVTPASQILLALKEKPAPELSLSSQDLELVAKEDP
          SRADLGDE.DA..TG.R...S...PASQILL.LKEK.APELSLS..DLE......P
Retrocopy SRADLGDERDAAETGVRKRSSDIMPASQILLVLKEKSAPELSLSGPDLEVGKHQGP

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	10.81 RPM
ERP005899_muscle	0.05 RPM	16.58 RPM
SRP017611_brain	0.00 RPM	14.57 RPM
SRP017611_kidney	0.00 RPM	20.69 RPM
SRP017611_liver	0.00 RPM	9.51 RPM
SRP030211_testis	0.03 RPM	4.51 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_211 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_211 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013535	1 retrocopy	retro_btau_211 ,
Homo sapiens	ENSG00000160049	1 retrocopy	retro_hsap_3926,
Gorilla gorilla	ENSGGOG00000012721	1 retrocopy	retro_ggor_2642,
Pongo abelii	ENSPPYG00000001899	1 retrocopy	retro_pabe_3242,