RetrogeneDB ID: retro_pabe_2425

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:12981411..12983085(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AB1
• Ensembl ID: ENSPPYG00000016655
• Aliases: None
• Description: heat shock protein HSP 90-beta [Source:RefSeq peptide;Acc:NP_001126444]

Sequence

>retro_pabe_2425
ATGCCTGAGGAAGTGCACCATGGAGAGGAGGAGGTGGAGACTTTTGCCTTTCAGGCAGAAATTGCCCAACTCATGTCTCT
CATCATCAATACCTTCTATTCCAATGAGGAGATTTTCCTTCGGGAGTTGATATCTAATGCTTCTGATGCCTTGGACAAGA
TTCGCTATGAAAGCCTAACAGACCCTTCCAAGTTGGACAGTGGTAAAGAGCTGAAAATTGACATCATCCCCAATACTCAG
GAACATACCCTGACTTTGGTAGACATAGGCATTGGCATGACCAAAGCTGATCTCATAAATAATTTGGGAACCATTGCCAA
GTCTCGTACTAAAGCATTCATGGAAGCTCTTTAGGCTGGTGCAGACATCTCCATGATTGGGCAATTTGGTGTTGGTTTTA
TTCTGCCTACCTGGTAGCAGAGAAAGTGGTTGTGATCACAAAGCCCAATGATGATGGTATGCCTGGGAGTCTTCTGCTGG
AGGTTCCTTCACTGTGTGTGCTGACCATGGCGAGCCTATTGGCAGGGGTACCAAAGTGATCCTCCACCTTAAAGAAGATC
AGACAGAGTACTTAGAAGAGAGGCAGGTCAAAGAAGTAGTGAAGAAGCACTCTCGGTTCCTAGGCTATCCCATCACCCTT
TATCTGGAGAAGGAACAAGAGAAAGAAATTAGTGATGATAAGGCAGAGGAAGAGAAAGGTTAGAAAGAAGAGGAAAATAA
AGATGATGAAGAAAAGCCCAAGATCGAAGATATGGGTTCAGAAGAGGAGGATGACAGTGGTAAGGATAAGAAGAAGAAAA
CTAAGAAGATAAAAAAGAAATACATTGATCAGAAAGAACTAAACAAGACCAAGCCTATTTGGACCAGAAACGCTGAAGAC
ATCACCCAAGAGGAGTATGGAGAATTCTATAAGAGCCTCACCAATGACTGGAAAGACCACTTGGCAGTCAGGTACTTTTC
TGTAGAAGGTCAGTTGGAATTCAGAGCATTGCTATTCATTCCTCATCAGGCTCTCTTTGATCTTTTTGAGAACAAGAAGA
AAAAGAACAACATCAAACTCTATGTCCATCGTGTGTTCATCAGGGACAGCTGTGATGAGTTGACACCAGAGTGTCTCAAC
TTTATCCGTGGTGTGGTTGACTCTAAGGATTTGCCCCTGAACATCTCCCAAGAAATGCTCCAGCAGAGCAAAATCTTGAA
AGTCATTCACAGAAACATTGTTAAGAAGTGCCCTGAGCTCTTCGCTGAGCTGGTGGAAGACAAGGAGAATTACAAGAAAT
TCTATGAGGCATTCTCTAAAAATCTCAAGCTTGGAATCCACGAGGACTCCACTAACTGATGCCACCCATCTGAGCTGCTG
TGTTATCACACCTCCCAGTCTGGAGATGAGATGACATCTTTGTCAGAGTATGTTTCTCGCATGAAGGAGATACAGAAGTC
CATCTATTACATCACTGGTGAGAGCAAAGAGCAGGTTGCCAACTCAGCTTTTGCGGAGCGAGTATGGAAGCGGGGTTTCA
GGGTGGTATATATGACTGAGCCCATTGACGGCTACGTGTGAAGCAACTCGAGGAGTTTGATGGGGAGAGCCTGGTCTCAG
TTACCAAGGAGGGCCTGGAGCTACCTGAGGATGGGGAGGAGAAGAAGAGAATGGAAGAGAGGAAGGCAAAGTTT

Alignment

ORF - retro_pabe_2425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 77.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKE
          MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSN.EIFLRELISNASDALDKIRYESLTDPSKLDSGKE
Retrocopy MPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNEEIFLRELISNASDALDKIRYESLTDPSKLDSGKE

Parental  LKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGF-YSAYLV
          LKIDIIPN.QE.TLTLVD.GIGMTKADLINNLGTIAKS.TKAFMEAL.AGADISMIGQFGVGF.YSAYLV
Retrocopy LKIDIIPNTQEHTLTLVDIGIGMTKADLINNLGTIAKSRTKAFMEAL*AGADISMIGQFGVGF<YSAYLV

Parental  AEKVVVITKHNDDEQ-YAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQF
          AEKV.V......D...YAWESSAGGSFTV.ADHGEPIGRGTKVILHLKEDQTEYLEER.VKEVVKKHS.F
Retrocopy AEKV-VVITKPNDDG<YAWESSAGGSFTVCADHGEPIGRGTKVILHLKEDQTEYLEERQVKEVVKKHSRF

Parental  IGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYID
          .GYPITLYLEKE.EKEISDD.AEEEKG.KEEE.KDDEEKPKIED.GS.EEDDSGKDKKKKTKKIK.KYID
Retrocopy LGYPITLYLEKEQEKEISDDKAEEEKG*KEEENKDDEEKPKIEDMGSEEEDDSGKDKKKKTKKIKKKYID

Parental  QEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKK
          Q.ELNKTKPIWTRN..DITQEEYGEFYKSLTNDW.DHLAV..FSVEGQLEFRALLFIP..A.FDLFENKK
Retrocopy QKELNKTKPIWTRNAEDITQEEYGEFYKSLTNDWKDHLAVRYFSVEGQLEFRALLFIPHQALFDLFENKK

Parental  KKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSE
          KKNNIKLYV.RVFI.DSCDEL.PE.LNFIRGVVDS.DLPLNIS.EMLQQSKILKVI..NIVKKC.ELF.E
Retrocopy KKNNIKLYVHRVFIRDSCDELTPECLNFIRGVVDSKDLPLNISQEMLQQSKILKVIHRNIVKKCPELFAE

Parental  LAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITG
          L.EDKENYKKFYEAFSKNLKLGIHEDSTN....SELL.YHTSQSGDEMTSLSEYVSRMKE.QKSIYYITG
Retrocopy LVEDKENYKKFYEAFSKNLKLGIHEDSTN*CHPSELLCYHTSQSGDEMTSLSEYVSRMKEIQKSIYYITG

Parental  ESKEQVANSAFVERVRKRGFEVVYMTEPIDEYC-VQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESK
          ESKEQVANSAF.ERV.KRGF.VVYMTEPID.Y..V.QL.EFDG.SLVSVTKEGLELPED.EEKK.MEE.K
Retrocopy ESKEQVANSAFAERVWKRGFRVVYMTEPIDGYV<VKQLEEFDGESLVSVTKEGLELPEDGEEKKRMEERK

Parental  AKF
          AKF
Retrocopy AKF

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	1001.09 RPM
SRP007412_cerebellum	0.12 RPM	799.65 RPM
SRP007412_heart	0.00 RPM	514.20 RPM
SRP007412_kidney	0.00 RPM	545.93 RPM
SRP007412_liver	0.03 RPM	429.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2425 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2425 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2912
Pan troglodytes	retro_ptro_1968
Macaca mulatta	retro_mmul_1869

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
Gorilla gorilla	ENSGGOG00000008889	2 retrocopies	retro_ggor_1011, retro_ggor_701,
Macropus eugenii	ENSMEUG00000013735	1 retrocopy	retro_meug_1896,
Myotis lucifugus	ENSMLUG00000005239	2 retrocopies	retro_mluc_1604, retro_mluc_865,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Otolemur garnettii	ENSOGAG00000011961	1 retrocopy	retro_ogar_2574,
Pongo abelii	ENSPPYG00000006153	1 retrocopy	retro_pabe_1760,
Pongo abelii	ENSPPYG00000016655	2 retrocopies	retro_pabe_2425 , retro_pabe_415,
Pan troglodytes	ENSPTRG00000018217	4 retrocopies	retro_ptro_1850, retro_ptro_1968, retro_ptro_2003, retro_ptro_880,
Tupaia belangeri	ENSTBEG00000014873	1 retrocopy	retro_tbel_1428,