RetrogeneDB ID: retro_pabe_238

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:45684695..45685542(+)
• Located in intron of: ENSPPYG00000000315

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEF1
• Ensembl ID: ENSPPYG00000001611
• Aliases: None
• Description: penta-EF-hand domain containing 1 [Source:HGNC Symbol;Acc:30009]

Sequence

>retro_pabe_238
ATGGCCAGCTATCTGTATGGGCAGGGCTGCCCCGGAGATGCAGGGCAAGCGCCAGGAACCCCTCCAGGTAGCTACTACCT
TGGACCCCCCAATAGTGGAGGGCAGTATGGCAGCATGCTACCCCCTGGTGGTGGTTATGGGGATCCTGCCCCTGGAGGGC
CTTATGGACCACCAGCTAGTAGAGGGCCCTATGGACACCTCAATCCTGGGATGTTCCCCTCTGGAACTCCAGGAGGACCA
AATGATTGTACAGCTCCAGGGGGCCCCTACGGTCAGCCACCTCCAAATTCCTACGGTGCCCAGCAGCCCAGGCCTCATGG
ACAGGGTGGCTCCCCTCCCAATATGGATGAGGCCTACTCCTGGTTCCAGTCGGTGACTGATTACAGTGGCTTTATCTCCA
TGAAGGAGGTGAAGCAGGCTCTGGTCAACTGCAACTGGTCCTTGTTCAATGATGAGACCTGCCTCATGACAATAAACATG
TTTGACAAGACCTGATCAGGCCACATCAATGTCTATGGCTTCTCAGCCCTGTGGAAATTCATCCAGCAGTGGAAGCAGCT
CTTCTAGCAGTTATGACCGCAACAACTCAGGCTCCATTAGCTACACAGAGCTGCAGCAAGCTCTGTCCCAAATGGGCTAC
AACCTGAGCCCCCAGTTCACCCAGCTACTGGTCTCCAGCTACTGCCCACGCTCTGTCAATCCTGCCAGGCAGCTTGATTG
CTTCATCCAGGTGTGCACCCAGCTGCAGGTGCCGACAGAGGCCTTCCGGGAGAAGGACACAGCTGTACAAGGCAACATTC
GGCTCAGCTTCAAGGACGTCGTCACCATGACAGCTTCTCGGATGCTA

Alignment

ORF - retro_pabe_238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASYPYRQGCPGAAGQAPGAPPGSYYPGPPSSGGQYGSGLPPGGGYGGPAPGGPYGPPAGGGPYGHPNPG
          MASY.Y.QGCPG.AGQAPG.PPGSYY.GPP.SGGQYGS.LPPGGGYG.PAPGGPYGPPA..GPYGH.NPG
Retrocopy MASYLYGQGCPGDAGQAPGTPPGSYYLGPPNSGGQYGSMLPPGGGYGDPAPGGPYGPPASRGPYGHLNPG

Parental  MFPSGTPGGPYGGAAPGGPYGQPPPSSYGAQQPGLYGQGGAPPNVDPEAYSWFQSVDSDHSGYISMKELK
          MFPSGTPGGP....APGGPYGQPPP.SYGAQQP...GQGG.PPN.D.EAYSWFQSV..D.SG.ISMKE.K
Retrocopy MFPSGTPGGPNDCTAPGGPYGQPPPNSYGAQQPRPHGQGGSPPNMD-EAYSWFQSV-TDYSGFISMKEVK

Parental  QALVNCNWSSFNDETCLMMINMFDKTKSGRIDVYGFSALWKFIQQWKNLFQQ-YDRDRSGSISYTELQQA
          QALVNCNWS.FNDETCLM.INMFDKT.SG.I.VYGFSALWKFIQQWK.LF.Q.YDR..SGSISYTELQQA
Retrocopy QALVNCNWSLFNDETCLMTINMFDKT*SGHINVYGFSALWKFIQQWKQLF*Q>YDRNNSGSISYTELQQA

Parental  LSQMGYNLSPQFTQLLVSRYCPRSANPAMQLDRFIQVCTQLQVLTEAFREKDTAVQGNIRLSFEDFVTMT
          LSQMGYNLSPQFTQLLVS.YCPRS.NPA.QLD.FIQVCTQLQV.TEAFREKDTAVQGNIRLSF.D.VTMT
Retrocopy LSQMGYNLSPQFTQLLVSSYCPRSVNPARQLDCFIQVCTQLQVPTEAFREKDTAVQGNIRLSFKDVVTMT

Parental  ASRML
          ASRML
Retrocopy ASRML

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	52.47 RPM
SRP007412_cerebellum	0.00 RPM	43.53 RPM
SRP007412_heart	0.09 RPM	15.98 RPM
SRP007412_kidney	0.07 RPM	35.73 RPM
SRP007412_liver	0.09 RPM	37.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_238 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_238 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_497
Pan troglodytes	retro_ptro_375
Gorilla gorilla	retro_ggor_464

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238 ,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,