RetrogeneDB ID: retro_btau_1363

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:103726254..103727180(-)
• Located in intron of: ENSBTAG00000017770

Retrocopy information

• Ensembl ID: ENSBTAG00000017766
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSBTAG00000002851
• Aliases: None
• Description: None

Sequence

>retro_btau_1363
GAAATGATGTTAGACCAAAAGTAAATTCGAGCAATTTTCTTAATTCGAGTTCAAAATGGGTTGTAAAACAGCAGCAACAA
CTTGAAACATCAATAACCCATTTGGCCCAGGAACTGCTAACGAACATACAGTGCAGTGGTGGTTTAAGAAGTTTTGCAAG
GGAGATGAGAGCCTTGAAGGTGAGAAGTGCAGTGGTTGGCCATCAGAAGTTGATAACGATCAACTGAGAGCAATCATCAA
AGCTGATCCTCTTACAACTACACAAGAAGTTGCTGAAAGAACTCAGCGTCAATCATTCTATGGTCATTTGGCATTTGAAG
CAAATTGGAAAGGTGAAAAGCTCGATAAGTGGGTGCCTCATGAACTGATCGAAAATTTTAAAAACCGTCATTTTGAAGTG
TCATCTTCTCTTATACTGTGCAACAGCAACGAACCATTTCTTAATCAGATTGTGACATGTGACAAAAAGTGGATTTTATA
TGACAACCAGCTCAGTGGTTGGACTGAGAAGAAGCTCCAAAGCACTTGCCAAAGCCAAGCTTGCACCAAAAAAAGGTCAT
GGTCACTGTTTGGTCTGCTGCCAGTCTGATCCACTACAGCTTTTTGAATCTCTGGGAAACCATTACACCCGAGAAGTATG
CTCAGCACATTGATGAGAGGCTCGGGAAACTGCAACGCCTGCAGCTGGCATTGGTCAACAAAAAGGGCCCAGTTCTTCTC
CACCAGAATGCCCAACTGCACATCACACAACCAGTGCTTCAAAAGTACTACGGATTGGGCTACGAAGTTTTGCCTCATCT
GCCATATTCACCTGACCTCTCGCCAACCAACTACCACTTCTTCAAGCATCTCAACAAATTTTGCAGGGAAAACGCTTCCA
CAACCAGCAGGAGGCAGAAAATGCTTTCCAGGAGTTCATGGGATCC

Alignment

ORF - retro_btau_1363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.34 %
• Parental protein coverage: 98.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EMMLDKKQIRMIFL-FKFKLGHKAMETICNINNAFSPGTANECTVQWCFKKFCKRDESLE-EEHGGLPSE
          EMMLD.K.IR.IFL.F.FK.G.K...T..NINN.F.PGTANE.TVQW.FKKFCK.DESLE.E...G.PSE
Retrocopy EMMLDQK*IRAIFL>FEFKMGCKTAATT*NINNPFGPGTANEHTVQWWFKKFCKGDESLEGEKCSGWPSE

Parental  ADNDQL-SRSSKLIILQVQEKLPQELNVNHSMVIWHLKQIGKVK-KLSKRALHAAACFMSQKQIKMMSSL
          .DNDQL...SSKLI.LQ...KL..EL.VNHSMVIWHLKQIGKVK.KL.K...H..............SSL
Retrocopy VDNDQL>EQSSKLILLQLHKKLLKELSVNHSMVIWHLKQIGKVK<KLDKWVPHELIENFKNRHFEVSSSL

Parental  SLCNNSEPFLN-RLWHVIKSELYTTTGN--NQRRSSKALPKAKLTP-KNVVVTVWWSAAGLTHYNFLNPS
          .LCN..EPFLN.RL.HV.KS..Y.TT......RRSSKAL.KAKL.P.K.V.VTV.WSAA.L.HY.FLN..
Retrocopy ILCNSNEPFLN>RL*HVTKSGFYMTTSSVVGLRRSSKALAKAKLAP>KKVMVTV-WSAASLIHYSFLNLW

Parental  ETITSEKNGQQISEVNQKLQSLQAVLLNRKGPVLFHDNTQLHVSANA-SKVSKLGYKVLPHPPYSPEDLW
          ETIT.EK..Q.I.E...KLQ.LQ..L.N.KGPVL.H.N.QLH.......K...LGY.VLPH.PYSP.DL.
Retrocopy ETITPEKYAQHIDERLGKLQRLQLALVNKKGPVLLHQNAQLHITQPVLQKYYGLGYEVLPHLPYSP-DLS

Parental  PIEYHFFKHLH-NFQGKC-FHKQQEAENAFQKFIES
          P..YHFFKHL..NF.GK..FH.QQEAENAFQ.F..S
Retrocopy PTNYHFFKHLN>NFAGKT>FHNQQEAENAFQEFMGS

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	2.02 RPM	0.00 RPM
ERP005899_muscle	0.48 RPM	0.00 RPM
SRP017611_brain	1.00 RPM	0.00 RPM
SRP017611_kidney	1.36 RPM	0.00 RPM
SRP017611_liver	0.15 RPM	0.00 RPM
SRP030211_testis	2.47 RPM	0.17 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1363 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1363 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1363 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002851	9 retrocopies	retro_btau_1096, retro_btau_1110, retro_btau_1177, retro_btau_1204, retro_btau_1363 , retro_btau_1525, retro_btau_392, retro_btau_831, retro_btau_846,