RetrogeneDB ID: retro_pabe_1279

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:28262417..28263879(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HCN1
• Ensembl ID: ENSPPYG00000015446
• Aliases: None
• Description: hyperpolarization activated cyclic nucleotide-gated potassium channel 1 [Source:HGNC Symbol;Acc:4845]

Sequence

>retro_pabe_1279
TACAGAGACTTCACCATGCTGCTGTTCATGGTGGGAAACCTCATCATCCCAGTGGGCATCACCTTCTTCAAGGACGAGAC
CACCGCCCTGTGGATCGTGTTCAACGTGGTCTCGGACACCTTCTTCCTCATGGACCCGGTGTTGAACTTCCACACCGGCA
TTGTGATCGAGGACAACACGGAGATCATCCTGGACCCCAAGAAGATCAAGAAGAAGTACCTGCGCAAGTGGTTCGTGGTG
GACTTCGTGTCCTCCATCCCCGTGGACTACATCTTTCTCATCGTGGAGAAGGGCATGGACTCCGAGGTCTACAAGACGGC
GTGCGCCCTGCGCATCGTGAGCTTCACCAAGATCCTCAACCTCCGGTGGCTGCTGGGCCTCTCGCACCTGATCCGATACA
TCCACCAGTGGGAGATCTTCCACATGACCTATGACCTGGCCAGCGCGGTGATGCGGATCTGCAACCTCATCAGTATGATG
CTGCTGCTCTGCCACTGGGATGGCTGCCTGCAGTTCCTGGTGGCCATGCTGCAGGACTTCCCGTGCAACTGCTGGGTGTC
CATCAATGGCATGGTGAACCACTAGTGTAGCCAACTGTATTCCTTCGCACTCTTCACGGCCATGAGCCACATGCTGTGCA
TTGGGTACGGCCGGCAGGCGCCCCAGAGCATGACGGACATCTGGCTGACCATGCTCAGCATGATTGTGGATGCCACCTGT
TACGCCATGTTCATCGGCTACGCCACTGCCCTCATCCAGTCGCTGGACTCCTCGCGGCGCCAGTACCAGGAGAAGTACGA
GCAGGTGGAGCAGTACATGTCCTTCCACAAGCTACCGGCCGACTTCCGCCAGAAGATCCACGACTACTACGAGCACCGTT
ACCAGGGCAAGATGTTCGACGAGGACAGCGTCCTGGGCGAGCTCAACAGGCCCCTGCAGGAGGAGATCGTCAACTTCAAC
TGCCGGAAGCTGGTGGCCTCCATGCCGCTGTTCGCCAGTGCTGACCCCAACTTCGTCACGGCCATGCTGACCAAGCTCAA
GTTCGAGGTCTTCCAGCCGGGTGACTACCTCATCCGCTAAGGCACCACGGGGAAGATGTACTTCATCCAGCACGGCGTGG
TCAGCGTGCTCGCTAAGGGCAACAAGGAGATGAAGCTGTTTGATGGCTCCTACTTCGGGGAGATCTGCCTGCTCACCCGG
GGCCACGCACGGTGAGCGTGCGGGCCAAACCTACTGCCGCCTCTATTCGCTGAGCGTGGACAACTTCAACGAGGTGCTGG
AGGAGTACCCCATGATGCGGCGCGCCTTCAAGACGGTGGCCATCCACCGCCTGGACCGCTTCCGCAAGAAGAATTCCATC
CTCCTGCACAAGGTGCAGCATGACCTCAACTCGGGCATATTCAACAACCAGGAGAACGCCATCATCCAGGAGATCGTCAA
GTACCACCGCGAGATGGTGCAG

Alignment

ORF - retro_pabe_1279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.09 %
• Parental protein coverage: 55.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YWDLIMLIMMVGNLVIIPVGITFFTEQTTTPWIIFNVASDTVFLLDLIMNFRTGTVNEDSSEIILDPKVI
          Y.D..ML..MVGNL.IIPVGITFF...TT..WI.FNV.SDT.FL.D...NF.TG.V.ED..EIILDPK.I
Retrocopy YRDFTMLLFMVGNL-IIPVGITFFKDETTALWIVFNVVSDTFFLMDPVLNFHTGIVIEDNTEIILDPKKI

Parental  KMNYLKSWFVVDFISSIPVDYIFLIVEKGMDSEVYKTARALRIVRFTKILSLLRLLRLSRLIRYIHQWEE
          K..YL..WFVVDF.SSIPVDYIFLIVEKGMDSEVYKTA.ALRIV.FTKIL.L..LL.LS.LIRYIHQWE.
Retrocopy KKKYLRKWFVVDFVSSIPVDYIFLIVEKGMDSEVYKTACALRIVSFTKILNLRWLLGLSHLIRYIHQWE-

Parental  IFHMTYDLASAVVRIFNLIGMMLLLCHWDGCLQFLVPLLQDFPPDCWVSLNEMVNDSWGKQYSYALFKAM
          IFHMTYDLASAV.RI.NLI.MMLLLCHWDGCLQFLV..LQDFP..CWVS.N.MVN......YS.ALF.AM
Retrocopy IFHMTYDLASAVMRICNLISMMLLLCHWDGCLQFLVAMLQDFPCNCWVSINGMVNH*CSQLYSFALFTAM

Parental  SHMLCIGYGAQAPVSMSDLWITMLSMIVGATCYAMFVGHATALIQSLDSSRRQYQEKYKQVEQYMSFHKL
          SHMLCIGYG.QAP.SM.D.W.TMLSMIV.ATCYAMF.G.ATALIQSLDSSRRQYQEKY.QVEQYMSFHKL
Retrocopy SHMLCIGYGRQAPQSMTDIWLTMLSMIVDATCYAMFIGYATALIQSLDSSRRQYQEKYEQVEQYMSFHKL

Parental  PADMRQKIHDYYEHRYQGKIFDEENILNELNDPLREEIVNFNCRKLVATMPLFANADPNFVTAMLSKLRF
          PAD.RQKIHDYYEHRYQGK.FDE...L.ELN.PL.EEIVNFNCRKLVA.MPLFA.ADPNFVTAML.KL.F
Retrocopy PADFRQKIHDYYEHRYQGKMFDEDSVLGELNRPLQEEIVNFNCRKLVASMPLFASADPNFVTAMLTKLKF

Parental  EVFQPGDYIIREGAVGKKMYFIQHGVAGVITKSSKEMKLTDGSYFGEICLLTKGR-RTASVRA-DTYCRL
          EVFQPGDY.IR.G..G.KMYFIQHGV..V..K..KEMKL.DGSYFGEICLLT.G..RT.SVRA..TYCRL
Retrocopy EVFQPGDYLIR*GTTG-KMYFIQHGVVSVLAKGNKEMKLFDGSYFGEICLLTRGH<RTVSVRA<QTYCRL

Parental  YSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLQKFQKDLNTGVFNNQENEILKQIVKHDRE
          YSLSVDNFNEVLEEYPMMRRAF.TVAI.RLDR..KKNSILL.K.Q.DLN.G.FNNQEN.I...IVK..RE
Retrocopy YSLSVDNFNEVLEEYPMMRRAFKTVAIHRLDRFRKKNSILLHKVQHDLNSGIFNNQENAIIQEIVKYHRE

Parental  MVQ
          MVQ
Retrocopy MVQ

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	22.95 RPM	51.09 RPM
SRP007412_cerebellum	9.12 RPM	34.53 RPM
SRP007412_heart	0.78 RPM	0.09 RPM
SRP007412_kidney	0.30 RPM	0.00 RPM
SRP007412_liver	0.18 RPM	0.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1279 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1279 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000015446	1 retrocopy	retro_pabe_1279 ,