RetrogeneDB ID: retro_btau_627

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:51291687..51292853(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT6
• Ensembl ID: ENSBTAG00000004291
• Aliases: SEPT6, SEPT11
• Description: Septin-6 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZN0]

Sequence

>retro_btau_627
GTCAGCCAGGGCTTCTGCTTCAACATCCTGTGGGTGGGAGAGACAGGTTTGGGCAAGTCCACCCTCATGGACACCCTGTT
CAACACCAAGGTCGGGGGGAGCCAACCACACACACACGGCCGGGTGTCCAGCTCCGGTCCAATACCTGTGACCTTCAAGA
GAGCAACATGGGGCTAAAGCTGACAATTGTTAACACAGTGGGCTTCGGGGACCAGATCAACAAGGAGGACAGCTACGAGT
CCGTCGTGGAATTCATCGGTGCCCAGTTTGAGGCCTACCTGTAGGAGGAGCTGCGGATCTGCAGGGTACTGAACACCTAC
CATGACTCTCGCATCCGTGCCCGCTTGTACTTCATCGCCCCCATGGGTCATTCCTTGAAGTCTCTGGACCGAGTGACTAT
GAAGAAGCTGGACAGTAAGGGGAACATCATCCCCATCATCATCAAATCAGATGCCATTTCTAAGAGTGAGCTAACCAAGT
TCAAAATCAAAATCACCAGCAAGCTTGTCAGCAGTGGAATCCAGATCTACCAGTTCCCTACAGATGACAAGTCAGCAGCA
GAGATCAACAGAACCGTGAACGCCCACCTGCCATTTGCTGTCAAGGGCAGCACAAAAGAACGGAAGATAGGTAAGAAGAT
GAAAGTGTGGTGGTATCCCTGGGGCACGGTGCAAGTTGAAAATGAAGCCCACTGTGACTTTATGAAGCTGCAGGATATGC
CGATCTGAGGCAACATGGAGGATCTCCAGGAGCAGACCCCTGGCCCACACTGTGAGCTGTACCGCCGCTGTAAGCTGGAG
GAGGTGGGCTTCAAGGACACCGACCCTGACAGCAAACCATTCAGTTTACAGGAGACGTATGAGGCCAAAAGGAATGAGTT
GCTAGAGGAGCTCCAAAAAAAAGAAGAGATGAGAAAGATTTTCGTCCAGAGAGTCAAAGAGAAAGAAGCTGAACTTAAAG
AGGCAGAGACAGAGCTGCATTAGAAGCTTGACCGTCTGAAGAAACTACACCAGGGTGAGAAGAAGAAGCTGGAGGATAAG
AAGAAATCCCTGGATGACAAAGTGGACGCTTTCAAACAGAGGAAAATGGCAGCTGAGCTGCTCCAGTTTCAGGGCTCCCA
GGTTGAAGGCTCACAGACTCTGAAAAGAGACAAAGAGAAGAAAAAC

Alignment

ORF - retro_btau_627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.4 %
• Parental protein coverage: 91.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSQGFCFNILCVGETGLGKSTLMDTLFNTKF-EGEPATHTQPGVQLRSNTYDLQESNVGLKLTIVSTVGF
          VSQGFCFNIL.VGETGLGKSTLMDTLFNTK...GEP.THT.PGVQLRSNT.DLQESN.GLKLTIV.TVGF
Retrocopy VSQGFCFNILWVGETGLGKSTLMDTLFNTKV<RGEPTTHTRPGVQLRSNTCDLQESNMGLKLTIVNTVGF

Parental  GDQINKEDSYKPIVEFIDAQFEAYLQEELKIRRVLHTYHDSRIHACLYFIAPTGHSLKSLDLVTMKKLDS
          GDQINKEDSY...VEFI.AQFEAYL.EEL.I.RVL.TYHDSRI.A.LYFIAP.GHSLKSLD.VTMKKLDS
Retrocopy GDQINKEDSYESVVEFIGAQFEAYL*EELRICRVLNTYHDSRIRARLYFIAPMGHSLKSLDRVTMKKLDS

Parental  KVNIIPIIAKSDAISKSELTKFKIKITSELVNNGVQIYQFPTDDESVAEINGTMNAHLPFAVIGSTEELK
          K.NIIPII.KSDAISKSELTKFKIKITS.LV..G.QIYQFPTDD.S.AEIN.T.NAHLPFAV.GST.E.K
Retrocopy KGNIIPIIIKSDAISKSELTKFKIKITSKLVSSGIQIYQFPTDDKSAAEINRTVNAHLPFAVKGSTKERK

Parental  IGNKMMKARQYPWGTVQVENEAHCDFVKLREMLIRVNMEDLREQTHSRHYELYRRCKLEEMGFKDTDPDS
          IG.K.MK...YPWGTVQVENEAHCDF.KL..M.I..NMEDL.EQT...H.ELYRRCKLEE.GFKDTDPDS
Retrocopy IGKK-MKVWWYPWGTVQVENEAHCDFMKLQDMPI*GNMEDLQEQTPGPHCELYRRCKLEEVGFKDTDPDS

Parental  KPFSLQETYEAKRNEFLGELQKKEEEMRQMFVQRVKEKEAELKEAEKELHEKFDRLKKLHQDEKKKLEDK
          KPFSLQETYEAKRNE.L.EL....EEMR..FVQRVKEKEAELKEAE.ELH.K.DRLKKLHQ.EKKKLEDK
Retrocopy KPFSLQETYEAKRNELLEEL-XXXEEMRKIFVQRVKEKEAELKEAETELH*KLDRLKKLHQGEKKKLEDK

Parental  KKSLDDEVNAFKQRKTAAELLQSQGSQAGGSQTLKRDKEKKN
          KKSLDD.V.AFKQRK.AAELLQ.QGSQ..GSQTLKRDKEKKN
Retrocopy KKSLDDKVDAFKQRKMAAELLQFQGSQVEGSQTLKRDKEKKN

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	1.59 RPM
ERP005899_muscle	0.00 RPM	19.69 RPM
SRP017611_brain	0.05 RPM	27.86 RPM
SRP017611_kidney	0.00 RPM	16.95 RPM
SRP017611_liver	0.00 RPM	1.13 RPM
SRP030211_testis	0.86 RPM	0.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_627 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_627 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	ENSBTAG00000002608	1 retrocopy	retro_btau_1185,
Bos taurus	ENSBTAG00000004291	1 retrocopy	retro_btau_627 ,
Macropus eugenii	ENSMEUG00000006112	1 retrocopy	retro_meug_1193,
Microcebus murinus	ENSMICG00000002769	1 retrocopy	retro_mmur_1065,