RetrogeneDB ID: retro_mdom_1487

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:294621138..294622017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAT
• Ensembl ID: ENSMODG00000020693
• Aliases: None
• Description: phosphoribosyl pyrophosphate amidotransferase [Source:HGNC Symbol;Acc:9238]

Sequence

>retro_mdom_1487
ATCTTGGAGGAGTGCAGTGTGTTTGGCTGCATCGCCTCAGGATAGTGGCCCAAGCAGCTGGATGTGCCCCATGTGATCAC
CCTGGGGCTCTTGGGGCTTCAAAACCGGAGACAGGAGAGTGCTGGGATTGTAACAAGTGATGGATATGGTTTAATGCCAA
CAATCTGAACACACAAGGGAATGGGACTCGTAAACCATGTGTTTACTGAAGATAATTTGAAGAAGCTGTATGTTTCAAAT
CTTGGAATTGGTCACACAAGGTATGCTACCACTGGAAACTGTAAATTAGAGAACTGTCAACCCTTTGTTGTTGAAACACT
CCATGGAAAGATTGCCGTGGCACACAATGGAGAATTAATAAATTCTGTTCATCTGAGGAGAAAGCTTCCGTGACATGCTG
TTGAATTGTCAACATGTTCTGACAGTGAAATGATTACTCAGTTGCTGACCTATACACCTCCACATGAAAGATATGACAGC
CCTAACTGGGTAGCAAGGATTAAAAATTTAATGAAGGAAGCCCCTACATCATATTCATGACTTATTATGCACAGAGATGT
TATTTATGCAGTAAGAGATCCTGACAGAAATCGTCCCCTGTGTATTGGATGTATTATTCCTGTATCTGATATAAATGGAA
GAGGAAAAAATAATTCTGAAACTGAAGGATGGGTGGTATCATCTGAATCCTGCAGTTTTTTATCTATTGGTACAGTGTAT
TATCATGAATTTTTACCAGGAGAAATTGTGAAAATATCTAGACATAATGTTCATCCTCTTGATACTGTACCGAGGTCTGG
GGGAGATCCAGTGGCTTTCTGTATCTTTGAATATGTTTATATTGCAAGACCAGATAATATATTTGAATGTCATATACAC

Alignment

ORF - retro_mdom_1487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.05 %
• Parental protein coverage: 56.13 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IREECGVFGCISSGEWPTQLDVPHVITLGLVGLQHRGQESAGIVTSDGYGLMPTIRTHKGMGLVNHVFTE
          I.EEC.VFGCI.SG.WP.QLDVPHVITLGL.GLQ.R.QESAGIVTSDGYGLMPTI.THKGMGLVNHVFTE
Retrocopy ILEECSVFGCIASG*WPKQLDVPHVITLGLLGLQNRRQESAGIVTSDGYGLMPTI*THKGMGLVNHVFTE

Parental  DNLKKLYVSNLGIGHTRYATTGNCELENCQPFVVETLHGKIAVAHNGELINSVHLRRKLLRHGVGLSTGS
          DNLKKLYVSNLGIGHTRYATTGNC.LENCQPFVVETLHGKIAVAHNGELINSVHLRRKL..H.V.LST.S
Retrocopy DNLKKLYVSNLGIGHTRYATTGNCKLENCQPFVVETLHGKIAVAHNGELINSVHLRRKLP*HAVELSTCS

Parental  DSEMITQLLAYTPPHEKDDSPDWVARIKNLMKEAPTSYSLLIMHRDVIYAVRDPYGNRPLCIGRLIPVSD
          DSEMITQLL.YTPPHE..DSP.WVARIKNLMKEAPTSYS.LIMHRDVIYAVRDP..NRPLCIG..IPVSD
Retrocopy DSEMITQLLTYTPPHERYDSPNWVARIKNLMKEAPTSYS*LIMHRDVIYAVRDPDRNRPLCIGCIIPVSD

Parental  INGRGKNNSETEGWVVSSESCSFLSIGAVYYREVLPGEIVKISRHNVQTLDVVPRSGGDPVAFCIFEYVY
          INGRGKNNSETEGWVVSSESCSFLSIG.VYY.E.LPGEIVKISRHNV..LD.VPRSGGDPVAFCIFEYVY
Retrocopy INGRGKNNSETEGWVVSSESCSFLSIGTVYYHEFLPGEIVKISRHNVHPLDTVPRSGGDPVAFCIFEYVY

Parental  FARPDSIFEGKKH
          .ARPD.IFE...H
Retrocopy IARPDNIFECHIH

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1487 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1487 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023644	2 retrocopies	retro_ecab_1113, retro_ecab_270,
Homo sapiens	ENSG00000128059	1 retrocopy	retro_hsap_2809,
Gorilla gorilla	ENSGGOG00000004608	1 retrocopy	retro_ggor_1953,
Monodelphis domestica	ENSMODG00000020693	1 retrocopy	retro_mdom_1487 ,
Nomascus leucogenys	ENSNLEG00000008762	1 retrocopy	retro_nleu_431,
Pongo abelii	ENSPPYG00000029568	1 retrocopy	retro_pabe_2306,
Pan troglodytes	ENSPTRG00000016080	1 retrocopy	retro_ptro_1903,
Tursiops truncatus	ENSTTRG00000010928	1 retrocopy	retro_ttru_794,