RetrogeneDB ID: retro_mdom_876

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:262117931..262118611(-)
• Located in intron of: ENSMODG00000007851

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSMODG00000017924
• Aliases: None
• Description: general transcription factor IIIC, polypeptide 6, alpha 35kDa [Source:HGNC Symbol;Acc:20872]

Sequence

>retro_mdom_876
ATGGAAGCTGCACTCTTCTTCGAAGGGAACGAGAAGCTGCTGGAGGTTTGGTTCTCCCGACGGCAGCCAGATGAGAGCAA
AGGATCTGGGGATCTCCGCACCATCCCAAGGTTTGAGTGGCACAAACTTTTGGAGAATGTGCATTGTTTAATCATAAGTG
TGACAAAACTGACAAGCAGGAAGCTTATGTACTCAGTGAGAGTAGCATGTTTGTCTCCAAGAGATGTTTCATTTTGAAGA
CATGTGGTACCACCCTCTTACTGCAAGCACTGGTCCCCCTGTTGGAGCTTGCTAGGGAGTACAGTGGGTTTGACTTGATT
CAAAGCTTCTTTTATTCTTGTAAGAATTTCATGAAGCCTTCCCACCAGTAGTACCCACACAGGAATTTCCAGGAAGAAGT
AGAATTCCTTAATGACATTTTCCCAAATGGAGCAGCATATTGTATGGGGTGTATGAATTCTGATTGCTCGTACTTGTACA
CTCTGGATTTTCCAGAGAGCTGAGTTATTAATCAGCCAGATCAGACACTGGAAATTCTGATGAGTGAGCTTGACCCAGCA
GTTATGGACCAGTTCTACATGAAAGATGGTGTTACTGCAAATGATGTCACTCGTGTGAGTGGAATTCATAACCTGATACT
GGGTTCTGTCATTGATGCTACAATGTTCAATCCTTGTGGG

Alignment

ORF - retro_mdom_876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.42 %
• Parental protein coverage: 67.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEAAHFFEGTEKLLEVWFSRQQPDESKGSGDLRTIPRFEWDKLLENVHCLIISVTK-TDKQEAYVLSESS
          MEAA.FFEG.EKLLEVWFSR.QPDESKGSGDLRTIPRFEW.KLLENVHCLIISVTK.TDKQEAYVLSESS
Retrocopy MEAALFFEGNEKLLEVWFSRRQPDESKGSGDLRTIPRFEWHKLLENVHCLIISVTK<TDKQEAYVLSESS

Parental  MFVSKRRFILKTCGTTLLLQALVPLLELAREYSGFDSIQSFFYSRKNFMKPSHQEYPHRNFQEEVEFLND
          MFVSKR.FILKTCGTTLLLQALVPLLELAREYSGFD.IQSFFYS.KNFMKPSHQ.YPHRNFQEEVEFLND
Retrocopy MFVSKRCFILKTCGTTLLLQALVPLLELAREYSGFDLIQSFFYSCKNFMKPSHQ*YPHRNFQEEVEFLND

Parental  IFPNGAAYCMGRMNSDCWYLYTLDFPESRVINQPDQTLEILMSELDPAVMDQFYMKDGVTANDVTRVSGI
          IFPNGAAYCMG.MNSDC.YLYTLDFPES.VINQPDQTLEILMSELDPAVMDQFYMKDGVTANDVTRVSGI
Retrocopy IFPNGAAYCMGCMNSDCSYLYTLDFPES*VINQPDQTLEILMSELDPAVMDQFYMKDGVTANDVTRVSGI

Parental  RDLIPGSVIDATMFNPCG
          ..LI.GSVIDATMFNPCG
Retrocopy HNLILGSVIDATMFNPCG

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_876 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_876 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 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003535	1 retrocopy	retro_amel_370,
Choloepus hoffmanni	ENSCHOG00000001496	1 retrocopy	retro_chof_1436,
Callithrix jacchus	ENSCJAG00000005248	2 retrocopies	retro_cjac_3118, retro_cjac_4098,
Dasypus novemcinctus	ENSDNOG00000014270	4 retrocopies	retro_dnov_1228, retro_dnov_1654, retro_dnov_377, retro_dnov_931,
Homo sapiens	ENSG00000155115	3 retrocopies	retro_hsap_3714, retro_hsap_4728, retro_hsap_4735,
Gorilla gorilla	ENSGGOG00000010681	1 retrocopy	retro_ggor_2511,
Myotis lucifugus	ENSMLUG00000013919	1 retrocopy	retro_mluc_897,
Macaca mulatta	ENSMMUG00000012709	3 retrocopies	retro_mmul_1700, retro_mmul_2520, retro_mmul_2524,
Monodelphis domestica	ENSMODG00000017924	1 retrocopy	retro_mdom_876 ,
Mustela putorius furo	ENSMPUG00000010179	1 retrocopy	retro_mputfur_182,
Nomascus leucogenys	ENSNLEG00000012846	3 retrocopies	retro_nleu_1237, retro_nleu_2122, retro_nleu_2552,
Pan troglodytes	ENSPTRG00000018502	3 retrocopies	retro_ptro_2516, retro_ptro_3145, retro_ptro_3149,
Tupaia belangeri	ENSTBEG00000017031	4 retrocopies	retro_tbel_2653, retro_tbel_3585, retro_tbel_631, retro_tbel_943,