RetrogeneDB ID: retro_btau_1489

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:32805619..32806425(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.62006
• Ensembl ID: ENSBTAG00000017021
• Aliases: None
• Description: DNA replication licensing factor MCM4 [Source:RefSeq peptide;Acc:NP_001068626]

Sequence

>retro_btau_1489
GCCTCCTTCCAGTGTCGGGTGTGCACCCACACTGTCCTGGTAGAGATGGGCCGGGTCAGACCACTGAGCCTGCAAATGTG
CCTGCTGCCCCCCCAGTGTGGTGCTGACCCACAACTGCCTTGTGTTCTCTGACAAGCAGAGGATCAGACTCCGAGAGTCT
CCTGAAAATATGCTTGCAGGGCAGATGCCTCATGGTGACATCCTTTTGCTCACAATGATATTGTTGACAAGGTTCATCTT
GGGGACAGAGTGAACATTACAGGCATCTATCCAGCTGTTCCTATTGAATCAATCCAGGAATGAGTCATGTGAAGTCTGCT
GACAGAAGCCTCATTGGTATCATTCATTATCAGAAAACGGAGGCAAAGTGTCTGCATGAAGGAGATAAAGAAGCAGAACA
GAAACTTTTTCAGAGAAGCATGTGAAATTGCTTAAAAAACTTTCCAGAAAAACAAGCATTTATAAGAGATTTGCTTCAGC
CTCAGGTCCAAGCAATTAAGAACAGAAAGATTTCAAAAAGGAAATCACTCCAGCTTTTCCGGGAAATAGAAAAGGGTTTT
AGTCACACAGGAAGAGGCAGATTTCATGCTGAGATCAGCCTCCTGCTGTGTGGCAACCCTGGGGCCAGCAAGTCCCAGCT
GCTGCAGTATGGGTACAGCCTGGTTCCCTGGGACCAGTGCACGCCTGGGAAGGGTTTCAGTGATGTTGGCCTGACAGTAT
ATGTAGTGAAAGACCCTGAGAGGGGATGGCTGGTACTGCAGACTGGTGCCCTTTTCCTGAGTGACAGTGGCATATGCTGT
ATTGAT

Alignment

ORF - retro_btau_1489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.68 %
• Parental protein coverage: 72.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AFFQCQVCAHTARVEIDR-GRIAEP-CVCERCHTSHSMALIHNRSVFSDKQMIKLQESPEDMPAGQTPHT
          A.FQC.VC.HT..VE..R.G...EP.C.C..C..S....L.HN..VFSDKQ.I.L.ESPE.M.AGQ.PH.
Retrocopy ASFQCRVCTHTVLVEMGR<GQTTEP<CKCACCPPS--VVLTHNCLVFSDKQRIRLRESPENMLAGQMPHG

Parental  VVL-FAHNDLVDKVQPGDRVHVTGIYRAVPIR-INPRVSNVKSVYKTHIDVIHYRKTDSKRLHGLDEEAE
          ..L.FAHND.VDKV..GDRV..TGIY.AVPI..INP..S.VKS.....I..IHY.KT..K.LH..D.EAE
Retrocopy DIL<FAHNDIVDKVHLGDRVNITGIYPAVPIE<INPGMSHVKSADRSLIGIIHYQKTEAKCLHEGDKEAE

Parental  QKLFSEKRVELLKELSRKPDIYERLASALAPSIYEHEDIKKGILLQLFGGTRKDFSHTGRGKFRAEINIL
          QKLF.......LK....K......L.......I.....I.K...LQLF....K.FSHTGRG.F.AEI..L
Retrocopy QKLFQRSM*NCLKNFPEKQAFIRDLLQPQVQAI-KNRKISKRKSLQLFREIEKGFSHTGRGRFHAEISLL

Parental  LCGDPGTSKSQLLQYVHNLVPRGQYTSGKGSSAVGLTAYVMKDPETRQLVLQTGALVLSDNGVCCID
          LCG.PG.SKSQLLQY...LVP..Q.T.GKG.S.VGLT.YV.KDPE...LVLQTGAL.LSD.G.CCID
Retrocopy LCGNPGASKSQLLQYGYSLVPWDQCTPGKGFSDVGLTVYVVKDPERGWLVLQTGALFLSDSGICCID

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	0.00 RPM
ERP005899_muscle	0.00 RPM	10.66 RPM
SRP017611_brain	0.00 RPM	2.24 RPM
SRP017611_kidney	0.00 RPM	1.90 RPM
SRP017611_liver	0.00 RPM	0.60 RPM
SRP030211_testis	0.20 RPM	30.68 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1489 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1489 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	ENSBTAG00000017021	1 retrocopy	retro_btau_1489 ,
Monodelphis domestica	ENSMODG00000010213	1 retrocopy	retro_mdom_1561,
Rattus norvegicus	ENSRNOG00000001833	1 retrocopy	retro_rnor_1549,
Vicugna pacos	ENSVPAG00000012049	1 retrocopy	retro_vpac_135,