RetrogeneDB ID: retro_mdom_1797

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:149416055..149416616(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGN
• Ensembl ID: ENSMODG00000000375
• Aliases: None
• Description: regucalcin [Source:HGNC Symbol;Acc:9989]

Sequence

>retro_mdom_1797
AGCAGGTGTGGAGAATTTCTAGTGTGGGAAGCAAAATCCCATAATATCCTGTTCATGAATATTCCATCCAAGAAGATTTG
CTGATGGGATTCACTCACCAATCAAGTACAAGAGGTCATATTAGATAGTCCAGTCAGCTTAGGGACCATTCAATAGTCTG
TTGGATGTATTGCAACTGTAGGGGCTCCATTTTGTTTTTTTAACTGGGAAGACCAATCACTATCTGATCTGGTTTCTATG
GATAAAGTTAAGAAAAACAATTGATTCAATTATGGGAAAATGGATTCAGCTGGGAGATACTTCCTTGGTACCTGGCCAAG
GAACCTGGCCCTGATATACTGGAGAGACAATAAGGTACCCTATATGCTCTCTTTCCTAATGGCAGTATAACAAAGAAGTA
CTTATCATGTGGACATCTCTAATGGTTTAGATTGGTCCCAGGATCACAAAAATTTCTCTTAAGTTGATAGTCTCTCTTAC
TCTGTGGATGTCTTTGATTATTATCTACAGACTGGAAAGATTACCAAATGCAGAAGTAGGTACAAGATGGAAAAAGAACA
G

Alignment

ORF - retro_mdom_1797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 62.54 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRCGESPLWEEKSNSLLFVDIPGKKICRWNSLTNQVQEIVIDSPATSVAIRQCGGYVATVGTRFCVVNWE
          SRCGE...WE.KS...LF..IP.KKIC.W.SLTNQVQE...DSP.....I....G..ATVG..FC..NWE
Retrocopy SRCGEFLVWEAKSHNILFMNIPSKKIC*WDSLTNQVQEVILDSPVSLGTIQ*SVGCIATVGAPFCFFNWE

Parental  NQLVSDLVSVDQDKKNNRFNDGKVDPAGRYFAGT-MAEETAPAVLERHQGSLYALFPNGTVKKYF-DNVD
          .Q..SDLVS.D..KKNN.FN.GK.D.AGRYF.GT..A.E..P..LER..G.LYALFPNG...K.....VD
Retrocopy DQSLSDLVSMDKVKKNN*FNYGKMDSAGRYFLGT<LAKEPGPDILERQ*GTLYALFPNGSITKKY>YHVD

Parental  ISNGLDWSLDHKIFYYIDSLSYSVDAFDYDLQTGLIVNRRSIYKMEKEE
          ISNGLDWS.DHK.F...DSLSYSVD.FDY.LQTG.I...RS.YKMEKE.
Retrocopy ISNGLDWSQDHKNFS*VDSLSYSVDVFDYYLQTGKITKCRSRYKMEKEQ

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_1797 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1797 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013028	1 retrocopy	retro_amel_915,
Canis familiaris	ENSCAFG00000014821	1 retrocopy	retro_cfam_685,
Monodelphis domestica	ENSMODG00000000375	1 retrocopy	retro_mdom_1797 ,
Mustela putorius furo	ENSMPUG00000013105	1 retrocopy	retro_mputfur_1618,