RetrogeneDB ID: retro_mdom_1752

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:210735525..210736632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_mdom_1752
CAACAACCCATCACTATGGCCCACCGTTTTCCAGCACTCACCCCCCCAGAAAAAGGAGGAGCTCTCAGACATTGCTGAAG
GCATTGTTGCTGATGGCAAGGGGATCCTGCCAGCAGATGCATCTGTTGGTACTATGGGCAATCGGCTGTAGAGGATCAAG
GTAGAGAACATAGAAGAAAACCGCCACCAGTTCTGAGAAATTCTCTTAACTGTGGTCAAATCCATCAACCAGAGCATTGG
AGGGGTGATCCTTTTCCATGAGAGTCTCTATCAGAAGGATAGCCAAGGAAAGTGGTTCAGAGACATCCTCAAGGAAAAGG
GGATTGTGGTAGGAATCAAGTTGGACCAAGGTGCTGCCCCCCTGGCAGGAACAAATCAATAAACAACTATTAAAGGCTTG
GATGGACTCTCTCAGTGCTGTGACCAGTATAAGAAGGACGGCTGTGACTTTGGGAAGTGGAGGGCTGTGCTAAAGATTGG
TGACCACTGTCCTTCAACCTGGCCATCCAGGAGAATGCTAATGAGCTGGCCTGCTCTGCCAGTATCTGCCAGCAGAATGG
GCTAGTGCCCATTGTGGAGCCAGAAGTCATCCCTGATGGTGATCATGACCTGGAACATTGCCAATATGTCTCTGAGAAGG
TCCTGGCTGCCATCTACAAGGCCCTGAGTGATCACCATGTCTACTTGGAAGGAATACTCCTGAAGCCCAACACGGTGACA
GCCGGGCATGCTCGCACCAAGAAGTACACCCCTGAACAGGTGGCTCTGGCTACCGTCACCACTCTGCACGGCACAGTCCC
AGCTGCTGTTCCTGGCATCTGCTTTCTATCTGGAGGCATGAGTGAAGAAGATGCGACTCTTAATCTAAATGCCATCAACC
TTTGCCCACTGCCCAAGCCCTGGAGGTTAAGTTTCTCATATGGGTGGGCCCAGCAGGCCAGTGCACTTTCTGCCTGGGGG
GGGCAAAGCTGCAAACAAGAAAGCAACTCAGGAGGCATTTGGGAGGCTGGTTCAGGCAAATGGCCAGGCAGCCAAAGGAC
AGTATATTCATTCAGGTTCATCTGGTTCTGTTGCCCGCCAATACCTTTCACTCCCTGCTACACCTAT

Alignment

ORF - retro_mdom_1752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 92.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RRPITMAHRFPALTP-EQKKELSDIAKRIVADGKGILAADESVGTMGNRLQRIKVENTEENRRQFREILF
          ..PITMAHRFPALTP...K.ELSDIA..IVADGKGIL.AD.SVGTMGNRL.RIKVEN.EENR.QF.EIL.
Retrocopy QQPITMAHRFPALTP>QKKEELSDIAEGIVADGKGILPADASVGTMGNRL*RIKVENIEENRHQF*EILL

Parental  TVDKSINQSIGGVILFHETLYQKDSQGKWFRDILKEKGIVVGIKLDQGAAPLAGTNQETTIQGLDGLSQR
          TV.KSINQSIGGVILFHE.LYQKDSQGKWFRDILKEKGIVVGIKLDQGAAPLAGTNQ.TTI.GLDGLSQ.
Retrocopy TVVKSINQSIGGVILFHESLYQKDSQGKWFRDILKEKGIVVGIKLDQGAAPLAGTNQ*TTIKGLDGLSQC

Parental  CAQYKKDGCDFGKWRAVLKIGDHCPS-NLAIQENANALARYASICQQNGLVPIVEPEVIPDGDHDLEHCQ
          C.QYKKDGCDFGKWRAVLKIGDHCPS.NLAIQENAN.LA..ASICQQNGLVPIVEPEVIPDGDHDLEHCQ
Retrocopy CDQYKKDGCDFGKWRAVLKIGDHCPS<NLAIQENANELACSASICQQNGLVPIVEPEVIPDGDHDLEHCQ

Parental  YVSEKVLAAVYKALSDHHVYLEGTLLKPNMVTAGHACPKKYTPEQVAMATVTTLHRTVPAAVPGICFLSG
          YVSEKVLAA.YKALSDHHVYLEG.LLKPN.VTAGHA..KKYTPEQVA.ATVTTLH.TVPAAVPGICFLSG
Retrocopy YVSEKVLAAIYKALSDHHVYLEGILLKPNTVTAGHARTKKYTPEQVALATVTTLHGTVPAAVPGICFLSG

Parental  GMSEEDATLNLNAINLCPLPKPWKLSFSYGRALQASALSA-WGGKAANKKATQEAFVKRALANGQAAKGQ
          GMSEEDATLNLNAINLCPLPKPW.LSFSYG.A.QASALSA....KAANKKATQEAF.....ANGQAAKGQ
Retrocopy GMSEEDATLNLNAINLCPLPKPWRLSFSYGWAQQASALSA>XXXKAANKKATQEAFGRLVQANGQAAKGQ

Parental  YIHSGSSGSAASQSL-FVPSYTY
          YIHSGSSGS.A.Q.L.F.P.YTY
Retrocopy YIHSGSSGSVARQYL<FTPCYTY

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_1752 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1752 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,