RetrogeneDB ID: retro_pabe_3730

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:25332098..25332947(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL1
• Ensembl ID: ENSPPYG00000004706
• Aliases: None
• Description: methyltransferase like 1 [Source:HGNC Symbol;Acc:7030]

Sequence

>retro_pabe_3730
GTAGAGAAACCCGGGACTGGGATCATGGCAGCTGAGACTTGGAACGTGGCCAGAGCAGAGGCCCCGCAGCCCCAGAAGCG
CTACTACCGGCAATGTGCTCACTCCAACCCCATGGCAGACTACACGCTGCGCTATCCTGTGAAGCCAGAGGAGATGGACT
GGTCTGAGCTATACCCAGAGTTCTTCGCTCCACTCACTCAAAATCAGAGCCACGATGACCCAAAGGATAAGAAAGAAAAG
AGAGCTCAGGCCCAAGCGGAGTCTGCAGACATAGGCTGTGGCTATGGTGGCCTGTTAGTGAAACTATCACCACTGTTCCC
AGACACACTGATTCTGGGTCTGGAGATCCAGGTGAAGGTCTCAGACTATGTACAAAACCGGATTTGGGCCCTACGCGCAG
CTCCTGGAGGTGGCTTCCAGAACACTGCCTGTCTCTGTAGCAATGCCATGAAGCACCTTCCTAACTTCTACAAGGCCAGC
TGACAAAGATATTCTTCCTCTTCCCTGACCCACATTTCAAGCAGACAAAGCACAAGCGGCAAATCATCAGTCCCACTCTG
CTAGCAAAATATGCCTACATGCTGAGAGTTGGGGGGCTGGTATATACCATAACCCATGTGCTGGAGCTACACGACTGGAT
GTGCACTCATTTTGAAGAGCACCCGCTGTTTGAGCGTATGCCTCTGGAGGACCTGAGTGAAGACCCCATTGTGGGACATC
TAGGTACCTCAACTGAGAAGGGGAAGAAAGTTCTATGTAATGGAGGGAAGAATTTCCCAGCCATCTTTCGAAGAATACAA
GATCCCGTCTTCTCAGGCAGTGACCCCCCAAACCAGCCTGCCTGGTCAC

Alignment

ORF - retro_pabe_3730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.51 %
• Parental protein coverage: 94.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEKPRTGIMAAETWNVAGAEAPPPQKRYYRQRAHSNPMADHTLRYPVKPEEMDWSELYPEFFAPLTQNQS
          VEKP.TGIMAAETWNVA.AEAP.PQKRYYRQ.AHSNPMAD.TLRYPVKPEEMDWSELYPEFFAPLTQNQS
Retrocopy VEKPGTGIMAAETWNVARAEAPQPQKRYYRQCAHSNPMADYTLRYPVKPEEMDWSELYPEFFAPLTQNQS

Parental  HDDPKDKNEKRAQAQVEFADIGCGYGGLLVELSPLFPDTLILGLEIRVKVSDYVQDRIRALRAAPAGGFQ
          HDDPKDK.EKRAQAQ.E.ADIGCGYGGLLV.LSPLFPDTLILGLEI.VKVSDYVQ.RI.ALRAAP.GGFQ
Retrocopy HDDPKDKKEKRAQAQAESADIGCGYGGLLVKLSPLFPDTLILGLEIQVKVSDYVQNRIWALRAAPGGGFQ

Parental  NIACLRSNAMKHLPNFFYK-GQLTKMFFLFPDPHFKRTKHKWRIISPTLLAEYAYVLRVGGLVYTITDVL
          N.ACL.SNAMKHLPN.FYK.GQLTK.FFLFPDPHFK.TKHK..IISPTLLA.YAY.LRVGGLVYTIT.VL
Retrocopy NTACLCSNAMKHLPN-FYK<GQLTKIFFLFPDPHFKQTKHKRQIISPTLLAKYAYMLRVGGLVYTITHVL

Parental  ELHDWMCTHFEEHPLFERVPLEDLSEDPIVGHLGTSTEEGKKVLRNGGKNFPAIFRRIQDPIL-QAVTPQ
          ELHDWMCTHFEEHPLFER.PLEDLSEDPIVGHLGTSTE.GKKVL.NGGKNFPAIFRRIQDP...QAVTPQ
Retrocopy ELHDWMCTHFEEHPLFERMPLEDLSEDPIVGHLGTSTEKGKKVLCNGGKNFPAIFRRIQDPVF>QAVTPQ

Parental  TSLPGH
          TSLPGH
Retrocopy TSLPGH

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	3.26 RPM
SRP007412_cerebellum	0.00 RPM	1.58 RPM
SRP007412_heart	0.00 RPM	1.35 RPM
SRP007412_kidney	0.00 RPM	10.01 RPM
SRP007412_liver	0.00 RPM	6.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3730 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3730 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3730 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4796
Gorilla gorilla	retro_ggor_2985
Macaca mulatta	retro_mmul_2556

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006615	1 retrocopy	retro_cjac_2888,
Homo sapiens	ENSG00000037897	1 retrocopy	retro_hsap_4796,
Gorilla gorilla	ENSGGOG00000001411	1 retrocopy	retro_ggor_2985,
Microcebus murinus	ENSMICG00000003803	1 retrocopy	retro_mmur_345,
Macaca mulatta	ENSMMUG00000022148	1 retrocopy	retro_mmul_2556,
Nomascus leucogenys	ENSNLEG00000017183	1 retrocopy	retro_nleu_1110,
Pongo abelii	ENSPPYG00000004706	1 retrocopy	retro_pabe_3730 ,
Tupaia belangeri	ENSTBEG00000011522	1 retrocopy	retro_tbel_3245,