RetrogeneDB ID: retro_mdom_393

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:378997057..378997743(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005581
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000014418
• Aliases: None
• Description: Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:F7BH72]

Sequence

>retro_mdom_393
TCTCTCAGCTGTGCCCAGTATAAGAAGGATGGCTGTGACTTTGGGAAGTGGAGGGCTGTGCTGAAGATTGGTGACCACTG
TCCTTCCAACCTGGCCATCCAGGAGAATGCTAATGAGCTGGCCCGCTATGCCAGTATCTCCCAGCAGAAAGGGCTGGTGC
CCATTGTGGAGCCAGAAGTCATCCCTGATGGCGATCATGACCTGGAGCATTGCCAATATGTCTCTGAGAAGGTCCTGGCC
TCCATCTACAAGGCCCTTAGTGACCACCACGTATACTTGGAGGGAATTCTCCTGAAGCAAAACATGGTGACAGCCGGGCT
TGCTTGCACCAAGAAGTACACCCCCAAACAGGTGGCTCTGGCTACCTTCACCACTCTGCACCGCACAGTCCCAGCTGCTG
TTCCTGGCATCTGCTTTCTATCTGGAGGCATGAGTGAAGAAGATGCGACTCTTAATCTAAATGCCATCAACCTTTGCCAA
CTGCCCAAGTCCTGGAAGCTAAGTTTCTCATATGGGCACACTCTGCAGGCCATTGCACTTTTTGCCTGGGGGGCAAAGCT
GCAAACAAGAAGGCAACTCAGGAGGCATTGATGAAGCAGGCTCAGACAAATGGCCAGGCAGCCAAAGGATAGTATATTCA
TTCAGGTTCATCTGGTTCTGCTGCCAGCCAATCCATTTTCACTCCT

Alignment

ORF - retro_mdom_393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 57.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQRCAQYKKDGCDFGKWRAVLKIGDHCPSNLAIQENANALARYASICQQNGLVPIVEPEVIPDGDHDLEH
          S..CAQYKKDGCDFGKWRAVLKIGDHCPSNLAIQENAN.LARYASI.QQ.GLVPIVEPEVIPDGDHDLEH
Retrocopy SLSCAQYKKDGCDFGKWRAVLKIGDHCPSNLAIQENANELARYASISQQKGLVPIVEPEVIPDGDHDLEH

Parental  CQYVSEKVLAAVYKALSDHHVYLEGTLLKPNMVTAGHACPKKYTPEQVAMATVTTLHRTVPAAVPGICFL
          CQYVSEKVLA..YKALSDHHVYLEG.LLK.NMVTAG.AC.KKYTP.QVA.AT.TTLHRTVPAAVPGICFL
Retrocopy CQYVSEKVLASIYKALSDHHVYLEGILLKQNMVTAGLACTKKYTPKQVALATFTTLHRTVPAAVPGICFL

Parental  SGGMSEEDATLNLNAINLCPLPKPWKLSFSYGRALQASALSAW-GGKAANKKATQEAFVKRALANGQAAK
          SGGMSEEDATLNLNAINLC.LPK.WKLSFSYG..LQA.AL.AW.GGKAANKKATQEA..K.A..NGQAAK
Retrocopy SGGMSEEDATLNLNAINLCQLPKSWKLSFSYGHTLQAIALFAW<GGKAANKKATQEALMKQAQTNGQAAK

Parental  GQYIHSGSSGSAASQSLFVP
          G.YIHSGSSGSAASQS.F.P
Retrocopy G*YIHSGSSGSAASQSIFTP

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	0.33 RPM	0.00 RPM
SRP007412_heart	0.20 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	57.40 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_393 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_393 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 5 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014816	5 retrocopies	retro_dnov_1625, retro_dnov_1631, retro_dnov_2028, retro_dnov_2152, retro_dnov_547,
Echinops telfairi	ENSETEG00000017395	2 retrocopies	retro_etel_2089, retro_etel_945,
Monodelphis domestica	ENSMODG00000014418	2 retrocopies	retro_mdom_1752, retro_mdom_393 ,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Tupaia belangeri	ENSTBEG00000009298	1 retrocopy	retro_tbel_3244,