RetrogeneDB ID: retro_pabe_3617

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:22504712..22505921(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL15
• Ensembl ID: ENSPPYG00000003399
• Aliases: METTL15, METT5D1
• Description: probable methyltransferase-like protein 15 [Source:RefSeq peptide;Acc:NP_001126687]

Sequence

>retro_pabe_3617
ATGCTTCAATATCCATATTTTTGTAGAATGTATAAAGAACATCTTTCATGTTGGTTGGAATCTGGCATACCTAATTTAGG
TGTCTGGCCAAAAAGAATACCTACTACAGCAGAAAAATATAAAGAATATGAAGCCCAGGAGCAAACAGATCAAACTCAAG
CCCAGGAGTTAAACAGATCTCAAGATAGAGATTTTGAAACTATGGCTAAATTACATATTCCGGTAATGGTGGATGAAGTT
GTTCATTGTTTGTCACCGCAAAAAGGACAGGTTTTTCTAGATATGATATTTGGTTCAGGAGGGCACACAAAAGCTATTCT
ACAGAAGGAGTCAGATATTGTTCTGTATGCCTTGGACAGAGACACAACAGCTTATGCATTAGCTGAACATCTTTCAGAGT
TGTATCCTAAACAAATCCGAGCTATGCTGGGCTAGTTCAGCCAGGCTAAAGCCTTATTAATGAAAGCTGGAGTGCAGCCA
GATACTTTTGATGGAGTTCTTATGGATCTTGGGTGTTCCTCCATGCAACTTGATACTCCCAAAAGAGGTTTTTCCCTTCA
GAAAGACGGCCCCTTAGACATGAGGATGGATGGTGGCAGGTACCTTGACATGCCCACTGCTGCTAATGTTGTGAATGCTT
TAGATCAACAGGTACTTGCATCTATCCTAAGAACATATGGGGAGGAGAAGCATGCCAAGAAAATCGCTTCAGCACACAGC
ATCTACCCCATCACCAGAACCAAGCAGCTTGCCAGCATCATCACAGGAGCATTTCCTCCCTCTGCTATTTATGCACGAAA
AGACTTGCTACAACAATCTACTCATATTGCCACCAAGACCTTCCAGGCTCTTCGCATATTTGTGAACAATGAGCTCAATG
AACTCTACACAGGACTGAAGACAGCTCAGAAGTTTCTGAGACCTGGTGGTTGCCTTGTTGCCCTCTCCTTCCATGCACTA
GAGGATTGCATCGTCAAAAGATTTTTGCTTGGAATAAGCATGACAGAAAGTTTTAACCTAAGTGTTAGACAGCAAGTGAT
GAAAACACTGCAACTGGGTTCAGATCATGAAAACACGGAAGAAGTCTCTATGAGAAGAGCTCCTTTCATGTGAGAATTGA
TACACAAGAAGGTACTTAGTCCACAAGATCGGGATGTACAAGATAACCCCAGAGGGTGCTCAGCCAAGCTTAGAGGAGCT
ATCAAATTA

Alignment

ORF - retro_pabe_3617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRYPYFCRMYKECLSCWLESGIPNLGVWPKTIHTTAEKYREYEAREQTDQTQAQELHRSQDRDFETMAK
          ML.YPYFCRMYKE.LSCWLESGIPNLGVWPK.I.TTAEKY.EYEA.EQTDQTQAQEL.RSQDRDFETMAK
Retrocopy MLQYPYFCRMYKEHLSCWLESGIPNLGVWPKRIPTTAEKYKEYEAQEQTDQTQAQELNRSQDRDFETMAK

Parental  LHIPVMVDEVLHCLSPQKGQIFLDMTFGSGGHTKAILQKESDIVLYALDRDPTAYALAEHLSELYPKQIR
          LHIPVMVDEV.HCLSPQKGQ.FLDM.FGSGGHTKAILQKESDIVLYALDRD.TAYALAEHLSELYPKQIR
Retrocopy LHIPVMVDEVVHCLSPQKGQVFLDMIFGSGGHTKAILQKESDIVLYALDRDTTAYALAEHLSELYPKQIR

Parental  AMLGQFSQAEALLMKAGVQPGTFDGVLMDLGCSSMQLDTPERGFSLRKDGPLDMRMDGGRYPDMPTAADV
          AMLG.FSQA.ALLMKAGVQP.TFDGVLMDLGCSSMQLDTP.RGFSL.KDGPLDMRMDGGRY.DMPTAA.V
Retrocopy AMLG*FSQAKALLMKAGVQPDTFDGVLMDLGCSSMQLDTPKRGFSLQKDGPLDMRMDGGRYLDMPTAANV

Parental  VNALDQQALASILRTYGEEKHAKKIASAIVQARSIYPITRTQQLASIVAGAFPPSAIYARKDLLQRSTHI
          VNALDQQ.LASILRTYGEEKHAKKIASA.....SIYPITRT.QLASI..GAFPPSAIYARKDLLQ.STHI
Retrocopy VNALDQQVLASILRTYGEEKHAKKIASA----HSIYPITRTKQLASIITGAFPPSAIYARKDLLQQSTHI

Parental  ATKTFQAVRIFVNNELNELYMGLKTAQKFLRPGGRLVALSFHSLEDRIIKRFLLGISMTERFNLSVRQQV
          ATKTFQA.RIFVNNELNELY.GLKTAQKFLRPGG.LVALSFH.LED.I.KRFLLGISMTE.FNLSVRQQV
Retrocopy ATKTFQALRIFVNNELNELYTGLKTAQKFLRPGGCLVALSFHALEDCIVKRFLLGISMTESFNLSVRQQV

Parental  MKTSQLGSDHENTEEVSKRRAPLMWELIHKKVLSPQDQDVQDNPRARSAKLRAAIKL
          MKT.QLGSDHENTEEVS.RRAP.M.ELIHKKVLSPQD.DVQDNPR..SAKLR.AIKL
Retrocopy MKTLQLGSDHENTEEVSMRRAPFM*ELIHKKVLSPQDRDVQDNPRGCSAKLRGAIKL

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	6.47 RPM
SRP007412_cerebellum	0.00 RPM	10.09 RPM
SRP007412_heart	0.00 RPM	5.18 RPM
SRP007412_kidney	0.03 RPM	6.76 RPM
SRP007412_liver	0.00 RPM	6.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3617 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3617 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4656

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006142	2 retrocopies	retro_cjac_3301, retro_cjac_4047,
Homo sapiens	ENSG00000169519	2 retrocopies	retro_hsap_1123, retro_hsap_4656,
Macaca mulatta	ENSMMUG00000013616	1 retrocopy	retro_mmul_870,
Nomascus leucogenys	ENSNLEG00000017865	2 retrocopies	retro_nleu_1093, retro_nleu_187,
Oryctolagus cuniculus	ENSOCUG00000014291	1 retrocopy	retro_ocun_536,
Pongo abelii	ENSPPYG00000003399	1 retrocopy	retro_pabe_3617 ,
Pan troglodytes	ENSPTRG00000003461	1 retrocopy	retro_ptro_680,