RetrogeneDB ID: retro_pabe_305

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:142302962..142304099(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COIL
• Ensembl ID: ENSPPYG00000008248
• Aliases: None
• Description: coilin [Source:HGNC Symbol;Acc:2184]

Sequence

>retro_pabe_305
GCCAAGAATCCCAAGTCTCCTAAAGTACAGGCAGTAAAAGACTGGGCCAATCAGAGATGTAGTTCTCCAAATGGTTCTGC
TAGAAACAGCCTTGTTAAAGCCAAAAGGAAAGGTAGTGTAAGCGTTTGCTCAAAAGAGAGTCCCAGTTCCTCCTCGGAGT
CTGAGTCTTGTGATGAATCTATCAGTGATGGTCCCAGCAAAGTCACTTTGGAGGCCAGAAATTCCTCAGAGAAATTACCA
ACTGAGTTATCAAAGGAAGAACCTTCTACCAAAAATACAACTGCAGACAAACTGGCTACAAAACCTGGCTTTAGCCTTAC
CCCCAGAAAGGGCAAGACCTCTGGAACGTCTTCTAGTTCAGACTCTAGTTCAGAGTCAGATGACCAATGCTTGATGTCAT
TGAGCACCCCGGAGTGTGCTGTGGGTTTCTTAAAGACAGTGGGCCTTTTTGCAGGAAGAGGTTGTCCAGGCCTAGGGCTG
TCATCACAGACTGAAGGTGCTGCTGGATGGAGGCATTCTGGCTCAAATGGTGGTGGACAGGCTCCTGGTCCTTCTCCCAG
TGTGTCTCTCCCCGCTAGTTTAGGAACAGGATGGGGTAGAGGAGAGAACCTTTTTTCTTGGAAGGAAGCTAGGGAATGGG
GCATGCGGGAGAGAGGTCGAGGATGAGGGCATCCTGTTTCCTGTGTTATAAATAGAAGCATTGACAACCAGAGGCAACAG
CAATTAAATGACGTGGTAACAAATTCATCTACTATTATCCAGAATCCAGTAGAGACACACAAGAAGGACTATAGTCTGTT
ACCACTGTTAGCAGCTGCCTCTCTAGTTGGAGAAAAGATTGCATTTAAGCTTTTGGAACTAACATCCAGTTACTCTCCTG
ATGTCTCTGACTACAAGGAAGGAAGAATATTAAGCCGCAACCCAGAGATCCAGCAAGTAGATACAGAAATTCTTTCATTC
TTACCTGCCTTGAGAGAACCTGGGAAATTTGATTTAGTTTATCACAATGAAAATGGAACCGAGGTAGTGGAGTACACTGT
GACACAGAAGAGCAAAATCACTGTATTTTGGAGAGAGTTGATTGACCCAAGACTGATAATTGAATCTCCAAGTAACACAT
CAAGTACAGAACCTGCC

Alignment

ORF - retro_pabe_305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.84 %
• Parental protein coverage: 74.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKNPKSPKVQAVKDWANQRCSSPKGSARNSLVKAKRKGSVSVCSKESPSSSSESESCDESISDGPSKVTL
          AKNPKSPKVQAVKDWANQRCSSP.GSARNSLVKAKRKGSVSVCSKESPSSSSESESCDESISDGPSKVTL
Retrocopy AKNPKSPKVQAVKDWANQRCSSPNGSARNSLVKAKRKGSVSVCSKESPSSSSESESCDESISDGPSKVTL

Parental  EARNSSEKLPTELSKEEPSTKNTTADQLAIKLGFSLTPSKGKTSGTTSSSSDSSSESDDQCLMSSSTPEC
          EARNSSEKLPTELSKEEPSTKNTTAD.LA.K.GFSLTP.KGKTSGT.SSSSDSSSESDDQCLMS.STPEC
Retrocopy EARNSSEKLPTELSKEEPSTKNTTADKLATKPGFSLTPRKGKTSGT-SSSSDSSSESDDQCLMSLSTPEC

Parental  AAGFLKTVGLFAGRGRPGPGLSSQTAGAAGWRRSGSNGGGQAPGPSPSVSLPASLGRGWGREENLFSWKG
          A.GFLKTVGLFAGRG.PG.GLSSQT.GAAGWR.SGSNGGGQAPGPSPSVSLPASLG.GWGR.ENLFSWK.
Retrocopy AVGFLKTVGLFAGRGCPGLGLSSQTEGAAGWRHSGSNGGGQAPGPSPSVSLPASLGTGWGRGENLFSWKE

Parental  ARGRGMRGRGRGRGHPVSCVVNRSTDNQRQQQLNDVVTNSSTIIQNPVETPKKDYSLLPLLAAAPQVGEK
          AR..GMR.RGRG.GHPVSCV.NRS.DNQRQQQLNDVVTNSSTIIQNPVET.KKDYSLLPLLAAA..VGEK
Retrocopy AREWGMRERGRG*GHPVSCVINRSIDNQRQQQLNDVVTNSSTIIQNPVETHKKDYSLLPLLAAASLVGEK

Parental  IAFKLLELTSSYSPDVSDYKEGRILSHNPETQQVDIEILSSLPALREPGKFDLVYHNENGAEVVEYAVTQ
          IAFKLLELTSSYSPDVSDYKEGRILS.NPE.QQVD.EILS.LPALREPGKFDLVYHNENG.EVVEY.VTQ
Retrocopy IAFKLLELTSSYSPDVSDYKEGRILSRNPEIQQVDTEILSFLPALREPGKFDLVYHNENGTEVVEYTVTQ

Parental  ESKITVFWRELIDPRLIIESPSNTSSTEPA
          .SKITVFWRELIDPRLIIESPSNTSSTEPA
Retrocopy KSKITVFWRELIDPRLIIESPSNTSSTEPA

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	0.00 RPM	8.96 RPM
SRP007412_cerebellum	0.12 RPM	16.54 RPM
SRP007412_heart	0.00 RPM	4.43 RPM
SRP007412_kidney	0.00 RPM	8.09 RPM
SRP007412_liver	0.00 RPM	6.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_305 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_305 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008740	1 retrocopy	retro_chof_1121,
Callithrix jacchus	ENSCJAG00000013960	1 retrocopy	retro_cjac_2240,
Dasypus novemcinctus	ENSDNOG00000023961	1 retrocopy	retro_dnov_1986,
Echinops telfairi	ENSETEG00000003687	1 retrocopy	retro_etel_1537,
Nomascus leucogenys	ENSNLEG00000008026	1 retrocopy	retro_nleu_1014,
Oryctolagus cuniculus	ENSOCUG00000011345	1 retrocopy	retro_ocun_1798,
Pongo abelii	ENSPPYG00000008248	1 retrocopy	retro_pabe_305 ,
Tupaia belangeri	ENSTBEG00000008882	4 retrocopies	retro_tbel_2118, retro_tbel_3549, retro_tbel_3961, retro_tbel_838,