RetrogeneDB ID: retro_pabe_2790

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:160277513..160278501(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ppy-mir-1181
• Ensembl ID: ENSPPYG00000009551
• Aliases: None
• Description: ppy-mir-1181 [Source:miRBase;Acc:MI0015181]

Sequence

>retro_pabe_2790
ATGGTGGACTACAGCATGTGGGACCACATAGAGGTGTCTGATGATGAAGACGAGACGCATGCCAACATGGACACGGCCAG
CCTCCTCCACTGGCAGCACCAGGCCCGGGGGGAGCGCATGGAGCAGTCCCAGAAGGAGAAGAGGAACCGGAAAGGGGCTG
CCATGAGTGCAAGCACAAGGTGGCCAAGTGCCAGAGGAAACTGAAGGAGCTGAAGGTGGCCGAGGGCGGCAAGGCAGAGC
TGGAGTGGCTGCAGGCCAAGGCACAGCAGCTACGCGAGGATCGGAGCTGGGAGCAGAAGCTGGAGGAGATGCACAAGAAG
GAGAAGAGTATGCCCTGGAACGTGGACATGCTCAGCAAAGACGGCTTCAGCAAGAACATGGTCAACACCAAACCTGAGAA
GGCCGAGGAGGACTCAGAGCAGGTGAGGGAGCAGAAACACAAGACCTTCGTGGAAAAGTACAAGAAACAGACCAAGAACT
TTGGCATGCTCGCCACTGGGATGACAGCCAAGAGTACCTGTCGGACAACGTCCACCTGGTGTGCGAGGAGACAGCCAATT
ACTTGGTCATCTGGTGCTTTGATCTAGAGGTGGAGAAGAAATGTGCACTCATGGAGCAGGTGGTCTCCCAGACAATCGTC
ATGTAGTTTATCCTGGAGCTGGCCAAGAGCCTGAAGGTGGACCCCCGGGCCTGCTTCCCGCAGTTCTTCGCTGAGATTAG
GACAGCCGATCGCCAGTACGTGGAGGGCTTCAACGACGATCTGGAAGCCTTCAAAGAATATGTGCGGGGCCGTGCCAAGC
TGCCCATCGAGAAGGCCATGAAGGAGTACAAGGAGGAGGAGCATGAGAAGCAGCTCGGCCCTGGCGGCCTGGACACCGTC
GAGGTCTACAAGTCCCTCCCTGAGGAACTCCAGAAGTGCTTCGATGTGAAAGATGTGCAGATGCTGCAAGACGCCATCAG
CAAGGGGGACCCCACCGACGCGAAGTAC

Alignment

ORF - retro_pabe_2790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 97.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVDYSVWDHIEVSDDEDETHPNIDTASLFRWRHQARVERMEQFQKEK-EELDRGCRECKRKVAECQRKLK
          MVDYS.WDHIEVSDDEDETH.N.DTASL..W.HQAR.ERMEQ.QKEK.EE..RGC.ECK.KVA.CQRKLK
Retrocopy MVDYSMWDHIEVSDDEDETHANMDTASLLHWQHQARGERMEQSQKEK<EEPERGCHECKHKVAKCQRKLK

Parental  ELEVAEGGKAELERLQAEAQQLRKEERSWEQKLEEMRKKEKSMPWNVDTLSKDGFSKSMVNTKPEKTEED
          EL.VAEGGKAELE.LQA.AQQLR.E.RSWEQKLEEM.KKEKSMPWNVD.LSKDGFSK.MVNTKPEK.EED
Retrocopy ELKVAEGGKAELEWLQAKAQQLR-EDRSWEQKLEEMHKKEKSMPWNVDMLSKDGFSKNMVNTKPEKAEED

Parental  SEEVREQKHKTFVEKYEKQIKHFGML-RRWDDSQKYLSDNVHLVCEETANYLVIWCIDLEVEEKCALMEQ
          SE.VREQKHKTFVEKY.KQ.K.FGML.R.WDDSQ.YLSDNVHLVCEETANYLVIWC.DLEVE.KCALMEQ
Retrocopy SEQVREQKHKTFVEKYKKQTKNFGML<RHWDDSQEYLSDNVHLVCEETANYLVIWCFDLEVEKKCALMEQ

Parental  VAHQTIVMQFILELAKSLKVDPRACFRQFFTKIKTADRQYMEGFNDELEAFKERVRGRAKLRIEKAMKEY
          V..QTIVM.FILELAKSLKVDPRACF.QFF..I.TADRQY.EGFND.LEAFKE.VRGRAKL.IEKAMKEY
Retrocopy VVSQTIVM*FILELAKSLKVDPRACFPQFFAEIRTADRQYVEGFNDDLEAFKEYVRGRAKLPIEKAMKEY

Parental  EEEERKKRLGPGGLDPIEVYESLPEELQKCFDVKDVQMLQDAISKMDPTTGSH
          .EEE..K.LGPGGLD..EVY.SLPEELQKCFDVKDVQMLQDAISK.DPT....
Retrocopy KEEEHEKQLGPGGLDTVEVYKSLPEELQKCFDVKDVQMLQDAISKGDPTDAKY

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	0.11 RPM	114.73 RPM
SRP007412_cerebellum	0.36 RPM	60.19 RPM
SRP007412_heart	0.09 RPM	47.08 RPM
SRP007412_kidney	0.27 RPM	74.75 RPM
SRP007412_liver	0.18 RPM	40.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2790 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2790 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2790 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3396
Macaca mulatta	retro_mmul_2113

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009437	1 retrocopy	retro_fcat_1338,
Homo sapiens	ENSG00000105401	1 retrocopy	retro_hsap_3396,
Gorilla gorilla	ENSGGOG00000008098	1 retrocopy	retro_ggor_2299,
Macropus eugenii	ENSMEUG00000002278	1 retrocopy	retro_meug_1373,
Macaca mulatta	ENSMMUG00000003111	1 retrocopy	retro_mmul_2113,
Pongo abelii	ENSPPYG00000009551	1 retrocopy	retro_pabe_2790 ,
Ictidomys tridecemlineatus	ENSSTOG00000015962	1 retrocopy	retro_itri_328,
Tursiops truncatus	ENSTTRG00000009560	1 retrocopy	retro_ttru_1073,