RetrogeneDB ID: retro_sscr_1200

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:69994596..69995693(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKT2
• Ensembl ID: ENSSSCG00000002989
• Aliases: AKT2, PRKBB
• Description: None

Sequence

>retro_sscr_1200
GGGGAGTACATCAAAACCTGGCTGCCCCAGTACTTCCTCCCAAAGAATGACACACCTTCATCAGCTACAAGGAGTGGCTG
CAGGACATGGAGCAGCGGGAGTCTCCCCTCAACTACTTCTCTGGCTCAATGCCAGCTGATGAAGACTAAGCAGTCACAGC
CCAACACCATCATCTGCTGCCTACAGTGGACCATGGCCATCCAGCACATATTTCATGTGGAGATGTCCAAGGAGTGGAAG
GAGTGGACGACTACCATCCAGATGGTGGCTGACGAGCTCAAGCAGCAGGGGGAAGAGATGATGGACTTCCAGTCGGGCTG
TCCCAGCAAGGACTTGTGGGCAGAGGAGATGGAGTTGTCCCTGTATAAGCCCAAACACCTCGTGACCATGAACGAGTTTG
AGTACCTGAAGCTGCTGGGCAAAGGTACCTTCAGGAAGGTGATCCTGGCAAAGGAGGAGGCCACCAGCAGCTACTACACC
ATGAAGATCCTGAAGAAAGAGGTAATTGTGGCCAGGGACGAGGTGGCCCACATGCTCACAGAGAACTGCATCCTCTAGAA
CTTCCAGCACCCCTTCCAGATGGCCCTGAAGTGCTCCTTCCAGACCTACGATTGCCTGTGCTTCATCATGGAGTATGCCA
ACAGGGATGAGCTCTTCTTCCACCTGTCCTGGGAGCAGGTGTTCCCTGAAGATGGGGGCCAGCTTCTATGGTGCTGAGAT
TGTGTCAGCCCTGGACTACTTGCACTCTGAGAAGGATATGGTGCACCAGGACCTCAAGCTGGAGAACCTCATGCTGGACA
AGGACAGGCACATCAAGATCATTGACTTCAGGCTCTGCAAGGAGGGCATCAAGGATAGTGCCACCATGAAGACATTCTGT
GGGATGCCGGAGTACCTGGTCACCGAGGTGTAGGAGGACAACAACTATGGCCAGGCAGTTGTCTGGTGGGGTGTGGGTGT
GGTCATGTATGAGATAATGTGCAGCCACCTGCCTTTTCTACAACCAGGACCATGAGAAGCTCTTCAAACTCATTCTCATG
AAGGAGATCCGCTTTCCGTGCATGCTCAGCCTTGAGGCCAAGTCTCTGCTCCAAGGA

Alignment

ORF - retro_sscr_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.34 %
• Parental protein coverage: 76.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GEYIKTWRPRYFLLKSDG-SFIGYKERPEAPDQTLPPLNNF-SVAECQLMKTERPRPNTFVIRCLQWTTV
          GEYIKTW.P.YFL.K.D...FI.YKE......Q...PL.N..S.A.CQLMKT....PNT..I.CLQWT..
Retrocopy GEYIKTWLPQYFLPKNDT<TFISYKEWLQDMEQRESPL-NY>SLAQCQLMKTKQSQPNT-IICCLQWTMA

Parental  IERTFHVDSPDEREEWMRAIQMVANSLKQRGAGEDPMDYKCGSPSDSSAAEEMEVAVSKARAKVTMNDFD
          I...FHV....E..EW...IQMVA..LKQ.G..E..MD...G.PS....AEEME....K....VTMN.F.
Retrocopy IQHIFHVEMSKEWKEWTTTIQMVADELKQQG--EEMMDFQSGCPSKDLWAEEMELSLYKPKHLVTMNEFE

Parental  YLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIAKDEVAHTVTESRVLQNTRHPFLTALKYAFQTHD
          YLKLLGKGTF.KVIL..E.AT..YY.MKIL.KEVI.A.DEVAH..TE...L.N..HPF..ALK..FQT.D
Retrocopy YLKLLGKGTFRKVILAKEEATSSYYTMKILKKEVIVARDEVAHMLTENCIL*NFQHPFQMALKCSFQTYD

Parental  RLCFVMEYANGGELFFHLSRERVFTEE-RARFYGAEIVSALEYLHS-RDVVYRDIKLENLMLDKDGHIKI
          .LCF.MEYAN..ELFFHLS.E.VF.E...A.FYGAEIVSAL.YLHS..D.V..D.KLENLMLDKD.HIKI
Retrocopy CLCFIMEYANRDELFFHLSWEQVFPED>GASFYGAEIVSALDYLHSEKDMVHQDLKLENLMLDKDRHIKI

Parental  TDFGLCKEGISDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLP-FYNQDHERLFE
          .DF.LCKEGI.D.ATMKTFCG.PEYL..EV.EDN.YG.AV.WWG.GVVMYE.MC..LP.FYNQDHE.LF.
Retrocopy IDFRLCKEGIKDSATMKTFCGMPEYLVTEV*EDNNYGQAVVWWGVGVVMYEIMCSHLP>FYNQDHEKLFK

Parental  LILMEEIRFPRTLSPEAKSLLAG
          LILM.EIRFP..LS.EAKSLL.G
Retrocopy LILMKEIRFPCMLSLEAKSLLQG

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	0.13 RPM	148.26 RPM
SRP014902_testis	0.14 RPM	183.46 RPM
SRP018288_heart	0.08 RPM	41.05 RPM
SRP018288_kidney	0.00 RPM	55.16 RPM
SRP018288_liver	0.00 RPM	85.07 RPM
SRP018288_lung	0.00 RPM	96.84 RPM
SRP018856_adipose	0.00 RPM	860.84 RPM
SRP035408_brain	0.00 RPM	29.95 RPM
SRP035408_liver	0.00 RPM	36.55 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1200 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1200 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014574	1 retrocopy	retro_cjac_1138,
Mus musculus	ENSMUSG00000004056	1 retrocopy	retro_mmus_694,
Sus scrofa	ENSSSCG00000002989	2 retrocopies	retro_sscr_1164, retro_sscr_1200 ,