RetrogeneDB ID: retro_mdom_467

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:713326612..713327004(+)
• Located in intron of: ENSMODG00000023058

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021273
• Aliases: None
• Description: None

Sequence

>retro_mdom_467
TCACAGAGGCACCCAGACATCCACATACAAGGAGAGAATTACCTCCCTCAAAAAATATATAGATACATACCATCTTTCCT
GTCAGTCTTCAAGCTAATATAATAGGCTTAATAATTGTTGGCAAAGATCCTTTTGCTTTCTTTGGCATGCAGGTTCCAAG
CTTCTGGCAGTGGGGTCAAGAAAATAAGATTTCTGCATGTATGATGGTTTTCTTCCTAAGAAACATGATTGAGAATCAGT
GTATGTCAACAGGTACATTTGAGATAACTCTAAATGATGCCCCATTGTGGACAAAGCTGGAATTTGGTCACCTTCCATCC
ATGTAGCATCTTATTCAAATTCTTGACAACAAAATGAAACTCAATGTGCATATACATTCAATCCCACATCAT

Alignment

ORF - retro_mdom_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 68.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQRYPDIRIEGENYLPQPIYRHIASFLSVFKLV-LIGLIIVGKDPFAFFGMQAPSIWQWGQENKIYACMM
          SQR.PDI.I.GENYLPQ.IYR.I.SFLSVFKL...IGLIIVGKDPFAFFGMQ.PS.WQWGQENKI.ACMM
Retrocopy SQRHPDIHIQGENYLPQKIYRYIPSFLSVFKLI<IIGLIIVGKDPFAFFGMQVPSFWQWGQENKISACMM

Parental  VFFLSNMIENQCMSTGAFEITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHH
          VFFL.NMIENQCMSTG.FEITLND.P.W.KLE.GHLPSM..L.QILDN.MKLNVH..SIPHH
Retrocopy VFFLRNMIENQCMSTGTFEITLNDAPLWTKLEFGHLPSM*HLIQILDNKMKLNVHIHSIPHH

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_467 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_467 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 18 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001394	2 retrocopies	retro_chof_1199, retro_chof_768,
Cavia porcellus	ENSCPOG00000002576	1 retrocopy	retro_cpor_459,
Equus caballus	ENSECAG00000025123	2 retrocopies	retro_ecab_441, retro_ecab_662,
Erinaceus europaeus	ENSEEUG00000013363	2 retrocopies	retro_eeur_63, retro_eeur_697,
Homo sapiens	ENSG00000198843	2 retrocopies	retro_hsap_3384, retro_hsap_4126,
Gorilla gorilla	ENSGGOG00000028291	1 retrocopy	retro_ggor_1892,
Macropus eugenii	ENSMEUG00000014738	3 retrocopies	retro_meug_1766, retro_meug_1786, retro_meug_2036,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467 ,
Mus musculus	ENSMUSG00000075700	1 retrocopy	retro_mmus_3111,
Nomascus leucogenys	ENSNLEG00000003284	2 retrocopies	retro_nleu_2473, retro_nleu_972,
Oryctolagus cuniculus	ENSOCUG00000013866	9 retrocopies	retro_ocun_1080, retro_ocun_1229, retro_ocun_1783, retro_ocun_1803, retro_ocun_1831, retro_ocun_327, retro_ocun_328, retro_ocun_557, retro_ocun_779,
Ochotona princeps	ENSOPRG00000014425	2 retrocopies	retro_opri_1052, retro_opri_584,
Pongo abelii	ENSPPYG00000029483	1 retrocopy	retro_pabe_3478,
Pan troglodytes	ENSPTRG00000039581	1 retrocopy	retro_ptro_2804,
Rattus norvegicus	ENSRNOG00000013507	1 retrocopy	retro_rnor_2069,
Sarcophilus harrisii	ENSSHAG00000018506	1 retrocopy	retro_shar_629,
Tarsius syrichta	ENSTSYG00000007410	3 retrocopies	retro_tsyr_1515, retro_tsyr_167, retro_tsyr_46,
Tursiops truncatus	ENSTTRG00000007522	2 retrocopies	retro_ttru_1556, retro_ttru_694,