RetrogeneDB ID: retro_sscr_25

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 12:30676640..30678695(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000017599
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KIF2C
• Ensembl ID: ENSSSCG00000003931
• Aliases: None
• Description: kinesin family member 2C [Source:HGNC Symbol;Acc:6393]

Sequence

>retro_sscr_25
ATGGCCAGCCATTTATGCCTCCCTGTCTCCTCGCGCCTCTCATCTGTGAAACCCTTGATGCTGCACTTTGGAAACGTACA
AGTGGGAGTCTGCGTGGCGATCCAGCGCAGTGATGGGCGGATCCATCTCGCAGTGGTCACGGAGGTTAAAAGAGAAAACA
CTTGGGTCACGGTAGAGTGGGTCGAAAAAGGAGTAAAAAAAGGCAAGAAGATTGATCTAGAGACCCTACTTCTGCTGAAT
CCAGCACTGGTCTCTGCTAAGCACCCCTCTCCAGGCAGGTCATTGTCCCGCTTGGCCCTAGCTCCCTCATCGGCCATTGG
GGACCAGCGAACGGCTGTACAGTGGATTGCTGCGATCCCCCAGAAAAACGAAACGCCCTCAGGGGACAACCTGGCCATGA
GAGTTCCCAGCAGTCCTTGCCTGATGAAGCAGAAAAAGTCTCCCTGCCTCCGGGAAATTGAGAAACTGCAAAAGCAGCGG
GAGAAGCGCAGACGGCTGCATCTGGATATCCAAGCCCAACGCGCCTTGGATGTCAACACGGGCAATCCCAGCTATGAGAT
AGGGCGCATGATTGCTGAGTACCGCAGGCACCTGGACCACAGCCAGATAGCCAGGCTGGAGCCGCCAGAGAACCACCGCA
TCTGCGTCTGCGTGAGGAAGCGGCCTCTCAACCAGCGGGAGACCACCATGAAGGACCTGGATATCATTACCATCCCCTCA
GACAATCTGGTCATGGTGCATGAGTCCAAGCAAAAAGTGGACCTCACTCGCTACCTGGAGAACCAGACTTTCTGTTTCGA
CCATGCCTTTGATCACACGGCCTCCAATGAGTTGGTGTACCAGTTCACCGCCCAACCGCTGGTCGAGTCCATCTTCCGAA
AAGGCATGGCCACCTGCTTTGCCTATGGGCAGACGGGCAGTGGGAAAACACACACCATGGGCGGAACATTTTCAAGAGGT
GACCAAGATTGTTCTAAAGGCATTTATGCCATGGTGGCGCGGGATGTCTTCCTCCTGCTCAAAACCTCCGCTTATGAGAA
TTTGGACCTCAAGGTCTATGGAACGTTTTTTGAGATTTATGGGGGCAAGGTGTATGACCTGTTGAACTGGAAGAAGAAGC
TGCAAGTCCTTGAAGATGGCAATCAGCAAATCCAGGTGGTCGGGCTGCAGGAGCAGGAGGTATGCTGTGTGGAGGACATG
CTGAACCTCGTGGAACTAGGGAACAGTTGCCGGACTTCAGGACAGACATCCGTCAATGCTCACTCTTCCAGGAGCCACGC
GGTGTTCCAGATCATCCTAAAGTCTCGAGGGAAACTCCATGGCAAATTTTCCCTTGTTGACTTAGCTGGGAATGAAAGGG
GAGTGGATACTGCCAAGGCCAACCGGAAAAGGCAGTTGGAAGGAGCAGAGATTAATAAGAGTCTCCTTGCACTCAAAGAA
TGCATCCGGGCTTTGGGTCAGAACAAGTCTCATACTCCATTCAGAGCCAGCAAGCTCACACAGGTGCTCCGGGACTCCTT
CATAGGCCAGAACTCCTCCACTTGCATGATCGCCACTATCTCTCCAGGGATGGCTTCTTGTGAAAACACCCTCAACACTT
TAAGATACGCAAACAGAGTAAAAGAAATAACTCTGGATTTAAGGCCTCACCATCGTTGCCTTTATCCTGCTGAACATGAG
GTGCCAAAGATGTTGAAAAGTCATAATAGAAATTCAGAAATGTCCTTTCAGAGATATGAATTTATTAAAGTGCCTTGTAC
ACAGAGTGAGGATAAGGAAGAGACTAGAGAAATCAAAGCATTATCCTCTTCTTTAATGAAGGATACAGCAATTGCCTTGA
AGGAATCAAGGCAATGGCCAGGGAAGGACATCCAGGAGACAGCTGATGGAGTAAACTGTGATGTTGATTTTTGCATTGCC
CAGTTATTGTCCATTTTGGAGCACAAAATAGATGTTCTAACTGAGATTAAAAGGAAACTGAAATTACTACAAGCTAATCT
TCAAATGAAAAACAAGTATAGTGAAGCCAATGATGAGAGATCAGATCTGAAATGA

Alignment

ORF - retro_sscr_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.01 %
• Parental protein coverage: 56.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANPVNSVRRKSCIVKEMEKMKNKREEKRAQNSEMRIKRAQEYDNSFPNWEFARMIKEFRATLDCHPLTVT
          ..P......KS....E.EK....RE..R.........RA.......P..E..RMI.E.R..LD.......
Retrocopy SSPCLMKQKKSPCLREIEKLQKQREKRRRLHLDIQAQRALDVNTGNPSYEIGRMIAEYRRHLDHSQIARL

Parental  DPIEEHRICVCVRKRPLNKQELAKKEIDVISVPSKCVLLVHEPKLKVDLTKYLENQAFCFDFAFDETASN
          .P.E.HRICVCVRKRPLN..E...K..D.I..PS.....VHE.K.KVDLT.YLENQ.FCFD.AFD.TASN
Retrocopy EPPENHRICVCVRKRPLNQRETTMKDLDIITIPSDNLVMVHESKQKVDLTRYLENQTFCFDHAFDHTASN

Parental  EVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGGGLYGKAQSASKGIYAMASQDVFLLKSQPRYR
          E.VY.FTA.PLV..IF..G.ATCFAYGQTGSGKTHTMGG......Q..SKGIYAM...DVFLL.....Y.
Retrocopy ELVYQFTAQPLVESIFRKGMATCFAYGQTGSGKTHTMGGTFSRGDQDCSKGIYAMVARDVFLLLKTSAYE

Parental  SLGLEVYVTFFEIYNGKLFDLLNKKAKLRVLEDGKQQVQVVGLQEHLVSCADDVIKMIDIGSACRTSGQT
          .L.L.VY.TFFEIY.GK..DLLN.K.KL.VLEDG.QQ.QVVGLQE..V.C..D.......G..CRTSGQT
Retrocopy NLDLKVYGTFFEIYGGKVYDLLNWKKKLQVLEDGNQQIQVVGLQEQEVCCVEDMLNLVELGNSCRTSGQT

Parental  FANSNSSRSHACFQILLRAKGRVHGKFSLVDLAGNERGADTSSADRQTRMEGAEINKSLLALKECIRALG
          ..N..SSRSHA.FQI.L...G..HGKFSLVDLAGNERG.DT..A.R....EGAEINKSLLALKECIRALG
Retrocopy SVNAHSSRSHAVFQIILKSRGKLHGKFSLVDLAGNERGVDTAKANRKRQLEGAEINKSLLALKECIRALG

Parental  QNKAHTPFRESKLTQVLRDSFIGENSRTCMIAMISPGISSCEYTLNTLRYADRVKELS
          QNK.HTPFR.SKLTQVLRDSFIG.NS.TCMIA.ISPG..SCE.TLNTLRYA.RVKE..
Retrocopy QNKSHTPFRASKLTQVLRDSFIGQNSSTCMIATISPGMASCENTLNTLRYANRVKEIT

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
SRP014902_placenta	0.00 RPM	1.33 RPM
SRP014902_testis	0.00 RPM	14.00 RPM
SRP018288_heart	0.00 RPM	1.73 RPM
SRP018288_kidney	0.00 RPM	2.56 RPM
SRP018288_liver	0.00 RPM	0.64 RPM
SRP018288_lung	0.00 RPM	10.39 RPM
SRP018856_adipose	0.52 RPM	0.05 RPM
SRP035408_brain	0.00 RPM	2.00 RPM
SRP035408_liver	0.00 RPM	12.51 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

4 EST(s) were mapped to retro_sscr_25 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW431469	30676606	30677107	99.7	499	2	497
CV869848	30676557	30677179	99.9	620	1	618
CV877044	30676597	30677171	99.5	571	3	568
CV877963	30676917	30677558	99.6	638	3	635

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_25 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_25 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028678	1 retrocopy	retro_mmus_1251,
Otolemur garnettii	ENSOGAG00000006916	1 retrocopy	retro_ogar_1892,
Pongo abelii	ENSPPYG00000001427	1 retrocopy	retro_pabe_88,
Pteropus vampyrus	ENSPVAG00000009856	1 retrocopy	retro_pvam_3,
Sus scrofa	ENSSSCG00000003931	1 retrocopy	retro_sscr_25 ,
Tursiops truncatus	ENSTTRG00000000748	1 retrocopy	retro_ttru_1318,
Drosophila melanogaster	FBgn0030268	2 retrocopies	retro_dmel_1, retro_dmel_2,