RetrogeneDB ID: retro_mdom_1017

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:225669015..225669645(+)
• Located in intron of: ENSMODG00000024865

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPRG1L
• Ensembl ID: ENSMODG00000006651
• Aliases: None
• Description: tumor protein p63 regulated 1-like [Source:HGNC Symbol;Acc:27007]

Sequence

>retro_mdom_1017
GGCTTAACAGGCAGTGGGCCTGGGGGCAGGACCCCAATGTGCCAGACACTGTGGCTGCTCATCATCCATGATCCCACGCA
CTGAGCCCGCATCAGGGAGTATTTTGTGTTCTAGCCCAGGACCATCAAAGAGGCTGTAGAGGAGTTCAGCTTAGTTGTCC
TGCCCACAGAGGATGGAGAGGTGTAGGGGGTATGGCTGCTTACTGAGATTGACCATTGGAAAAACAAAAAGGAACAGCTG
GTTCTCATTACAGATCAATCCCTTCTGATCTGTAAATATGACTTCATCAATCTATAATGCCAGCAGTTGGTCAAACTATC
ATTAAATATAATTGATACCATTTCCTATAGAGAGTTTGAGTTTCCTTCTAAGTCACTGAATAAGCAATGTTTTGGAATTC
AAATTCAGTGGGGAAAGCAAAGCTGCCCCTCCTTCATAAATAGATGGAATCTCTGGTCTACAAATCTGCCATATGCCACT
TTTATAGAGCACCCAATGGCAGATGACGATGAGAAGATTGCATCTCTTTGCCAATTGCAAAGCTTCAAGGCTCTATTAAT
TCAAGTCATCATAAAGGCCCAAAAGGAATTCCCTTTACCAGGTTGGACCAGTGGAGTGCTGGTCTTGGAG

Alignment

ORF - retro_mdom_1017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.41 %
• Parental protein coverage: 79.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVGAGGAGGRTPLRQTLWPLSVHDPTRRARVKEYFVFRTGTIEQAVEDIRLVVLPMEDGEVQGVWLLTEV
          G....G.GGRTP..QTLW.L..HDPT..AR..EYFVF...TI..AVE...LVVLP.EDGEV.GVWLLTE.
Retrocopy GLTGSGPGGRTPMCQTLWLLIIHDPTH*ARIREYFVF*PRTIKEAVEEFSLVVLPTEDGEV*GVWLLTEI

Parental  DHWNNEKERLVLITDQSFLICKYDFINLQCLQVVKISLNAIDTISYGQFEFPPKSLNKREGFGIRIQWDK
          DHW.N.KE.LVLITDQS.LICKYDFINL.C.Q.VK.SLN.IDTISY..FEFP.KSLNK...FGI.IQW.K
Retrocopy DHWKNKKEQLVLITDQSLLICKYDFINL*CQQLVKLSLNIIDTISYREFEFPSKSLNK-QCFGIQIQWGK

Parental  QSRPSFMNRWNPWSTNLPYATFIEHPMADADEKIASLCQLGSFKALLIQAVKRAQKEFPLPGRTNGLLVL
          QS.PSF.NRWN.WSTNLPYATFIEHPMAD.DEKIASLCQL.SFKALLIQ....AQKEFPLPG.T.G.LVL
Retrocopy QSCPSFINRWNLWSTNLPYATFIEHPMADDDEKIASLCQLQSFKALLIQVIIKAQKEFPLPGWTSGVLVL

Parental  E
          E
Retrocopy E

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_1017 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1017 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006651	1 retrocopy	retro_mdom_1017 ,
Pteropus vampyrus	ENSPVAG00000015273	1 retrocopy	retro_pvam_1018,
Ictidomys tridecemlineatus	ENSSTOG00000007466	1 retrocopy	retro_itri_28,
Tupaia belangeri	ENSTBEG00000011399	7 retrocopies	retro_tbel_1982, retro_tbel_2169, retro_tbel_2300, retro_tbel_2302, retro_tbel_2339, retro_tbel_2599, retro_tbel_2603,