RetrogeneDB ID: retro_pabe_2046

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:6227874..6228904(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000003246
• Aliases: None
• Description: None

Sequence

>retro_pabe_2046
CAGAGGAAGGCAGAGTATCCCGGCAGAGGAGGAGCAGCCCCCCGTGCCAGGCCTCCCGATGTCCCCAGGCTGCAGCCCCA
GGCCGCAAAATCCCCACCTCCAGTTCAGGGCAAGAAGAGTCCAAGACTCCTATGCCAACAACTGATAAAAATCCCAAAGA
AGGAAAAGAGGAAGATGATTCTGCCCTCCCTCAGTAAGTTTACATTGCTGCATCCAGACCTAGCCGGGGATGGTGCAGTA
GGAGCAGGACATGTGTTTCTCCTCATGGTGACACAGAGAACACCTGAAGCTTTTGGTGCAAGACTGGTTCATAGCAGCTC
GTCTGCAAATCAGAACCAAATACAGACCAACTCGATTATGATGTTGGAGAAGAGCATCAGTATCCAGGTGGCGTTAGCAA
GGAGGAAGAAGAAGAGACATTAATCAGTAAAGAGGAGATGCCATTCAAAGATGACCCAAGAGATGAGACCTACAAACCCC
TCTTAGAAAGGGAAACCCCAAAGCCACGCGAAAATCAGGGAAGGTGAAAGGAGAGAAGGAGAAGGAAATTAAAGTGGAAG
TACAGGTGGAGGTGAAAGAAGAGGAGAATGAAATTAGGGAGGATGAGGAACCTCCGAGGAAGAGAGGAAGAAGATGGAAA
GATGGCAAAAGTCCACATTTACCCAGAAGGAGAAAAAAGCCTCCAACCCAATATGTCCGTTGTGAGATGGAAGGATGTGG
AACTGTCCTTGCCCATCCTGGCTATTGACAGCACCACGTTAAATAGCATTTGTTGAAGAAAAAATATGTATGTCTGCATC
CCTCCTGTGGACGACTCTCTAGGCTCCAGAAGCAACTTCTGTGACATGCCAAACATCATACAGATCAAAGGGATTCTGTC
TGTGAATACTGTGCTCAGGCCTTCAAGAGTTCCCACAATCTGGTAGTGCACCAGATGATTCACATTGGCCAGAAGCCATT
ATTACAGTGTGAGATCTGTAAATTTACTTCTTGACAAAAGGCATCTCTTAATTGGCACATAAAGAAGCAT

Alignment

ORF - retro_pabe_2046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.69 %
• Parental protein coverage: 66.22 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRKAEYPRRRRSSPSSRPPDVPGQQPQAAKSPSPVQGKKSPRLLCIEKVTTDKDPKEE-KEEEDDSALPQ
          .RKAEYP.R....P..RPPDVP..QPQAAKSP.PVQGKKSPRLLC.......K.PK.E.KEE.DDSALPQ
Retrocopy QRKAEYPGRGGAAPRARPPDVPRLQPQAAKSPPPVQGKKSPRLLCQQLI---KIPKKE<KEE-DDSALPQ

Parental  EVSIAASRPSRGWRS-SRTSVSRHRDTENTRSSRSKTGSLQLICKSEPNTDQLDYDVGEEHQ-SSEEEEE
          .V.IAASRPSRGW.S.SRT.VS.H.DTENT.S...KTGS.QL.CKSEPNTDQLDYDVGEEHQ.......E
Retrocopy *VYIAASRPSRGWCSRSRTCVSPHGDTENT*SFWCKTGS*QLVCKSEPNTDQLDYDVGEEHQYPGGVSKE

Parental  EEEEMLISEEEIPFKDDPRDETYKPHLERETPKPR-RKSGKVKEEKEKKEIKVEVEVEVKEEENEIREDE
          EEEE.LIS.EE.PFKDDPRDETYKP.LERETPKPR.RKSGKVK.EKE.KEIKVEV.VEVKEEENEIREDE
Retrocopy EEEETLISKEEMPFKDDPRDETYKPLLERETPKPR<RKSGKVKGEKE-KEIKVEVQVEVKEEENEIREDE

Parental  EPPRKRGRRRKDDKSPRLPKRRKKPPIQYVRCEMEGCGTVLAHPRYLQHHIKYQHLLKKKYVCPHPSCGR
          EPPRKRGRR.KD.KSP.LP.RRKKPP.QYVRCEMEGCGTVLAHP.Y.QHH.K..HLLKKKYVC.HPSCGR
Retrocopy EPPRKRGRRWKDGKSPHLPRRRKKPPTQYVRCEMEGCGTVLAHPGY*QHHVK-*HLLKKKYVCLHPSCGR

Parental  LFRLQKQLLRHAKHHTDQRDYICEYCARAFKSSHNLAVHRMIHTGEKP-LQCEICGFTCRQKASLNWHMK
          L.RLQKQLL.HAKHHTDQRD..CEYCA.AFKSSHNL.VH.MIH.G.KP.LQCEIC.FT..QKASLNWH.K
Retrocopy LSRLQKQLL*HAKHHTDQRDSVCEYCAQAFKSSHNLVVHQMIHIGQKPLLQCEICKFTS*QKASLNWHIK

Parental  KH
          KH
Retrocopy KH

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
SRP007412_brain_prefrontal_cortex	0.17 RPM	26.43 RPM
SRP007412_cerebellum	0.49 RPM	37.09 RPM
SRP007412_heart	0.12 RPM	16.62 RPM
SRP007412_kidney	0.17 RPM	18.53 RPM
SRP007412_liver	0.03 RPM	10.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2046 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2046 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2046 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000003246	1 retrocopy	retro_pabe_2046 ,