RetrogeneDB ID: retro_btau_1805

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:23837531..23838403(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000002427
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SORD
• Ensembl ID: ENSBTAG00000025496
• Aliases: None
• Description: Sorbitol dehydrogenase [Source:UniProtKB/Swiss-Prot;Acc:Q58D31]

Sequence

>retro_btau_1805
ATGGCGGCAGCCAAGCCTGACGACCTCTGCTTGGTGGTGCATGGACCCAGAGACCTGCACTTGGAGTACTATCCTATCCC
TGAACCAGGCCCAAATGAGGTGCTACTGAAGATACATCCTGTCGGAATTTGTAGTTCAGATGTCCATGGCCGGCAGCATG
GTCGAATCAGAAATTTTGTTGTGAAAAAGCCAATGGTGCTAGGGCATAAAGCTTTGAGAACAGTCATAAAAGTGGAATCA
TCGGTCAAGCACTTATAACCAGGTGATCATGTTGACATTGAGCTTGGAGCTCCTTGAGAAACTTGATGAACTCTGCAAGA
CTGGCCGATACAATCTGTCACCAACCATCTTCTTCTGTGTCATGCCGCCCGATGATGGGAACCTCTGCCAGTTCTACAAG
CACAAGGCTAATTTCTGCTACAAGTTTCCTGACAATGTCACCTTTGAGGAAGGGGCCTTGGTTGAGCCACTGTCTGTGGG
GATTCATGCCTGCCGGCAAACTGGAAACAAGGTCCTTGTGTGTGGAGCTGGGCCAGATGGACTGGTCAGTTCCTCACAGC
CAAGGCGATGGGTGCAGCTCAAATGGTGGTGACTGATCTGTCAGCCTCTCGGTTGTCTAAAGCCAAGGAAGTTGGGGCTG
ATTTCATCCTCTGGACTCCAATGAGAGCCCTCAGGAAATAGCCAAGAAAGCAGAAGGTCTTCTGGGCAGCAAGCTGGAAG
TCACCATCAAGTGCACAGGAGCAGAGACCTCCATCCAGGCAGATATCTACCAGACTCATCCTGGTGGGCTGGTGCTGGTG
GTGCTGGGCTCTGAGATGACCAGTGGGCCCTTCGTGCATGCAGCCACCTGGAAGGTGGATATCAAGGGCATT

Alignment

ORF - retro_btau_1805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 83.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAAKPENLSLVVHGPGDLRLENYPIPEPGPNEVLLKMHSVGICGSDVHYWQHGRIGDFVVKKPMVLGHE
          MAAAKP..L.LVVHGP.DL.LE.YPIPEPGPNEVLLK.H.VGIC.SDVH..QHGRI..FVVKKPMVLGH.
Retrocopy MAAAKPDDLCLVVHGPRDLHLEYYPIPEPGPNEVLLKIHPVGICSSDVHGRQHGRIRNFVVKKPMVLGHK

Parental  ASGTVVKVGSLVRHLQPGDRVAIEPGAPRET-DEFCKIGRYNLSPTIFFCATPPDDGNLCRFYKHNANFC
          A..TV.KV.S.V.HL.PGD.V.IE.GAP.ET.DE.CK.GRYNLSPTIFFC..PPDDGNLC.FYKH.ANFC
Retrocopy ALRTVIKVESSVKHL*PGDHVDIELGAP*ET>DELCKTGRYNLSPTIFFCVMPPDDGNLCQFYKHKANFC

Parental  YKLPDNVTFEEGALIEPLSVGIHACRRAGVTLGNKVLVCGAGPIGLVS-LLAAKAMGAAQVVVTDLSASR
          YK.PDNVTFEEGAL.EPLSVGIHACR..G....NKVLVCGAGP.GLVS..L.AKAMGAAQ.VVTDLSASR
Retrocopy YKFPDNVTFEEGALVEPLSVGIHACRQTG----NKVLVCGAGPDGLVS<FLTAKAMGAAQMVVTDLSASR

Parental  LSKAKEVGADFILQI-SNESPQEIAKKVEGLLGSKPEVTIECTGVETSIQAGIYATHSGGTLVLVGLGSE
          LSKAKEVGADFIL...SNESPQEIAKK.EGLLGSK.EVTI.CTG.ETSIQA.IY.TH.GG.LVLV.LGSE
Retrocopy LSKAKEVGADFILWT<SNESPQEIAKKAEGLLGSKLEVTIKCTGAETSIQADIYQTHPGG-LVLVVLGSE

Parental  MTSVPLVHAATREVDIKGV
          MTS.P.VHAAT..VDIKG.
Retrocopy MTSGPFVHAATWKVDIKGI

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	91.85 RPM
ERP005899_muscle	0.00 RPM	53.63 RPM
SRP017611_brain	0.00 RPM	12.52 RPM
SRP017611_kidney	0.00 RPM	99.93 RPM
SRP017611_liver	0.00 RPM	94.99 RPM
SRP030211_testis	0.00 RPM	40.06 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1805 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1805 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1805 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025496	1 retrocopy	retro_btau_1805 ,
Ciona intestinalis	ENSCING00000021861	1 retrocopy	retro_cint_5,
Mustela putorius furo	ENSMPUG00000010850	1 retrocopy	retro_mputfur_201,
Mus musculus	ENSMUSG00000027227	2 retrocopies	retro_mmus_2795, retro_mmus_505,
Rattus norvegicus	ENSRNOG00000017291	7 retrocopies	retro_rnor_1272, retro_rnor_1813, retro_rnor_2021, retro_rnor_2022, retro_rnor_2023, retro_rnor_2024, retro_rnor_2857,