RetrogeneDB ID: retro_pabe_3296

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:153390217..153390869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED10
• Ensembl ID: ENSPPYG00000029389
• Aliases: TMED10, TMP21
• Description: transmembrane emp24 domain-containing protein 10 precursor [Source:RefSeq peptide;Acc:NP_001124930]

Sequence

>retro_pabe_3296
ATGTCTGGTTTGTCTGGCCCACCAGCCCGGCATGGCCCTTGTCTGTCGGCGTTGCTGCTTTTGTTCCTGCTGGGCCCCAG
CTTGGTCCTCGCCATCTCCTTCCATCTGCCCATTAACTCTCACAAGTGCCTCTGTGAGGAGATCCACAAGGACCTACTGG
TGACTGGCACATATGAGATCTCTGACCAGTCTGGCGGCACTGGCAGCCTGTGCAGCCACCTCAAGATCACAGATTCTGCT
GGCCATATTTTCTACTACAAAGAGAATGCAACCAAGGGGAAATTTGCCTTTACCACTGAAGATTATGACATGTTTGAAGT
GTGTTTTGAGAGCAAGGGAACAGGGCGGATACCTGACCAACTCGTGATCCTAGACATGAAGCATGGAGTGGAGGTGAAAA
ATTACAAAGAGATTGCAAAAGTTGAGAAGCTCAAACAATTAGAGGTGAAGCTGCGACACCTAGAAGACCTTTCAGAATAT
ATTGTTAATGGTTTTGCCTACATGAAGAAGAGAGAAGAGGAGATGGTGATACCAGTGAGTCAACAAACCCTTGGGTCCTA
TACTTCAGCATCTTTTCAATGTTCTGCCTCATTGGACTAGCCACCTGGCAGGTCTTCTACCTGTGATGCTTCTTCAAGGC
TACGAAGTTGAT

Alignment

ORF - retro_pabe_3296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSGLSGPPTRRGPFPLALLLLFLLGPSLVLAISFHLPINSRKCLREEIHKDLLVTGAYEISDQSGGAGGL
          MSGLSGPP.R.GP...ALLLLFLLGPSLVLAISFHLPINS.KCL.EEIHKDLLVTG.YEISDQSGG.G.L
Retrocopy MSGLSGPPARHGPCLSALLLLFLLGPSLVLAISFHLPINSHKCLCEEIHKDLLVTGTYEISDQSGGTGSL

Parental  RSHLKITDSAGHILYSKEDATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAKNYEEIAK
          .SHLKITDSAGHI.Y.KE.ATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVE.KNY.EIAK
Retrocopy CSHLKITDSAGHIFYYKENATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEVKNYKEIAK

Parental  VEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEM-RDTNXXXNTRVLY-SAS-FNVLSHWTSYLA-VFY
          VEKLK.LEV.LR.LEDLSE.IVN.FAYMKKREEEM..DT....N..VLY.SAS.FNVL.HWTS.LA.VFY
Retrocopy VEKLKQLEVKLRHLEDLSEYIVNGFAYMKKREEEM<GDTSESTNPWVLY>SAS>FNVLPHWTSHLA>VFY

Parental  -CDAS-QGQESD
          .CDAS.QG.E.D
Retrocopy >CDAS>QGYEVD

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	1.11 RPM	49.82 RPM
SRP007412_cerebellum	2.55 RPM	59.83 RPM
SRP007412_heart	1.69 RPM	57.17 RPM
SRP007412_kidney	2.06 RPM	74.25 RPM
SRP007412_liver	4.16 RPM	112.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3296 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3296 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4014
Pan troglodytes	retro_ptro_2724
Macaca mulatta	retro_mmul_2316

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016899	1 retrocopy	retro_acar_187,
Callithrix jacchus	ENSCJAG00000020627	2 retrocopies	retro_cjac_1409, retro_cjac_4223,
Dasypus novemcinctus	ENSDNOG00000019851	1 retrocopy	retro_dnov_1225,
Echinops telfairi	ENSETEG00000010607	1 retrocopy	retro_etel_1798,
Homo sapiens	ENSG00000170348	2 retrocopies	retro_hsap_2701, retro_hsap_4014,
Gorilla gorilla	ENSGGOG00000007453	1 retrocopy	retro_ggor_2696,
Myotis lucifugus	ENSMLUG00000017125	2 retrocopies	retro_mluc_2079, retro_mluc_2093,
Macaca mulatta	ENSMMUG00000015168	2 retrocopies	retro_mmul_2316, retro_mmul_885,
Mus musculus	ENSMUSG00000021248	2 retrocopies	retro_mmus_1093, retro_mmus_649,
Nomascus leucogenys	ENSNLEG00000016453	2 retrocopies	retro_nleu_2897, retro_nleu_2963,
Oryctolagus cuniculus	ENSOCUG00000004669	1 retrocopy	retro_ocun_875,
Pongo abelii	ENSPPYG00000029389	1 retrocopy	retro_pabe_3296 ,
Pan troglodytes	ENSPTRG00000006552	2 retrocopies	retro_ptro_1823, retro_ptro_2724,
Rattus norvegicus	ENSRNOG00000007901	2 retrocopies	retro_rnor_1729, retro_rnor_2031,
Ictidomys tridecemlineatus	ENSSTOG00000007392	1 retrocopy	retro_itri_362,
Vicugna pacos	ENSVPAG00000003089	1 retrocopy	retro_vpac_573,