RetrogeneDB ID: retro_pabe_2584

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:190022319..190022993(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNH
• Ensembl ID: ENSPPYG00000015619
• Aliases: None
• Description: cyclin-H [Source:RefSeq peptide;Acc:NP_001153279]

Sequence

>retro_pabe_2584
CACTCCTGGATAATAATGCTCACATGTGCATTTTTGGCCTACAAAGTAGATAAACTGAATGTATCTAGTCCCCAATTTGT
TGGAAACCTTCGGGAGAGTTCTCTCGTACAGGAGGAGACACTTGGACAGAGTTTGGAATATGAACTACATTTTATATAGC
AACGTAAATTTCCATCTGACTGTCCACAACCCCTACAGACCACTGGAGTGCTTCCTCACTGATTTAAAGACTTACTATGC
AATGCTGGAGAATCCAGACATTTTGAGGAAAACAGATGATGAACTCCTTAGTAGAATCACATTGATGGCTGCTTACCATT
TATACACACCTTCCCAAATTGCCCTGCCTGCCATTTTATCTAGTGCCTTCAGGGCTGGAATTACTATGGAAAGTTATTTA
TTGGACAATCTGATGTTGAGAGAGAACAGAACTTGCTTGTCACAGTTACTAGATATAATGAAAAGCATGAGAAATTGAGT
AAAAAAAGTATGTACCACCCAGATCTGAAGAAGCTGCTGTTCTGAAACTGAAGTTGGAGCAATGTCATTCTGCAGAGCTT
GCACTTAATGTAATTATGAAGAAGATGAAAGGCTGTGAAGATAATGATGATGTCTCAAAGAAATCCAGACATGAGGAGGA
AGAATAGACTGATGATGACCTGGTAGACTCTCTC

Alignment

ORF - retro_pabe_2584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.99 %
• Parental protein coverage: 69.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYEL-LLIQQLNFHLIVHNPYRPFE
          H..IIMLTCAFLA.KVD..NVSSPQFVGNLRES.L.QE..L.Q.LEYEL..L....NFHL.VHNPYRP.E
Retrocopy HSWIIMLTCAFLAYKVDKLNVSSPQFVGNLRESSLVQEETLGQSLEYEL>ILYSNVNFHLTVHNPYRPLE

Parental  GFLIDLKTRYPVLENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLML
          .FL.DLKT.Y..LENP.ILRKT.D..L.RI.L..AY.LYTPSQIAL.AILSSA.RAGITMESYL...LML
Retrocopy CFLTDLKTYYAMLENPDILRKTDDELLSRITLMAAYHLYTPSQIALPAILSSAFRAGITMESYLLDNLML

Parental  RENRTCLSQLLDIMKSMRNLV-KKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKS
          RENRTCLSQLLDIMKSMRN.V.KKY.PPRSEE.AVLK.KLE.CHSAELALNVI.KK.KG.ED.D.VSKKS
Retrocopy RENRTCLSQLLDIMKSMRN*V>KKYVPPRSEEAAVLKLKLEQCHSAELALNVIMKKMKGCEDNDDVSKKS

Parental  KHEEEEWTDDDLVESL
          .HEEEE.TDDDLV.SL
Retrocopy RHEEEE*TDDDLVDSL

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	0.06 RPM	10.01 RPM
SRP007412_cerebellum	0.00 RPM	9.61 RPM
SRP007412_heart	0.00 RPM	6.59 RPM
SRP007412_kidney	0.00 RPM	6.40 RPM
SRP007412_liver	0.00 RPM	7.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2584 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2584 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3128
Pan troglodytes	retro_ptro_2116
Gorilla gorilla	retro_ggor_2143
Macaca mulatta	retro_mmul_1991

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007765	1 retrocopy	retro_dnov_1618,
Homo sapiens	ENSG00000134480	1 retrocopy	retro_hsap_3128,
Gorilla gorilla	ENSGGOG00000005172	1 retrocopy	retro_ggor_2143,
Macaca mulatta	ENSMMUG00000003248	1 retrocopy	retro_mmul_1991,
Mus musculus	ENSMUSG00000021548	1 retrocopy	retro_mmus_2510,
Nomascus leucogenys	ENSNLEG00000013604	1 retrocopy	retro_nleu_2248,
Oryctolagus cuniculus	ENSOCUG00000004659	1 retrocopy	retro_ocun_588,
Pongo abelii	ENSPPYG00000015619	2 retrocopies	retro_pabe_2584 , retro_pabe_2590,
Pan troglodytes	ENSPTRG00000017063	1 retrocopy	retro_ptro_2116,
Ictidomys tridecemlineatus	ENSSTOG00000000659	1 retrocopy	retro_itri_856,