RetrogeneDB ID: retro_mdom_1210

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:494529146..494530782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2H1
• Ensembl ID: ENSMODG00000006540
• Aliases: None
• Description: general transcription factor IIH, polypeptide 1, 62kDa [Source:HGNC Symbol;Acc:4655]

Sequence

>retro_mdom_1210
ATGGCAACTTCATCAGAAGAAGTTTTACTGATTGTAAAAAAGATTTGCCAAAAGAAGCAGGATGGAGCCCTGTGCCTCAT
GGCAGAAAGGATTGCTTGGGCACCTGAAGGCAAAGACAGATTTACAATCAGCCTTTTGTATGCAGACATTAAATGCCAGA
AAATCAGTCCAGAATGAAAAGCAAAAATCCAGCTTCAGCTGGTGCTCCATGCAGGAGACACAACCAACTTCCATTTCTCC
AATGACAGTGCAGCTGTCAAGGAGCGAGATGCTGTGATAGATCTTCTTCAGGAGTTGCTATCAAGATTCAAGAGGAAAGC
CAAGAAAGAACTGAAAAAGAAAAAATAGAATGCTGCAAGAGGATCCTACTTTGTTTCAGCTTTATAAAGACTTGGTGGTG
AGTCAGGTGATCAGTGCTGAGGAATTCTGGGCTAGTGGTTTAAGGGCGGATACTATGGATAGCCCTGCAGCATCCAATCA
CAAGCAAGATGTGGGCATTTCTTCAGCATTTCTGGCTGATGTCTGCCCTCAGACAGATGGCTGTAATAGCCTAAGGTATA
ATTTAACCTCTGATATTATCGACTCCATATGTAGGACCTACCCAATAGTAAAACTGAAACATGCAGAGAATGTTCCACAT
AACATGACAGAAAAAGTGTTCTGGGCAAGATTTTTTCAATCCCATTATTTTCATAGGGATCAGCTCAATATAGGGTCACA
ACACCTCTTTGCAGAATGTGCCAAAATGGATGAAAAGGGTTTAAAGACAGTGGTATCTCTAGGAGTGAAAAACCCACTAC
TAGAGTTGACAGCCCTGGAGGATAAATCATTAGATGAGGGCTATGGAGTTTCTCCTGGACCATGTACTCAAAATCTTCAA
AATCCATGAAGGAGAATAACAATGCAGCAATCATCAAGAGATTTAACCACCACAATGCCATGGTCCTGGCAGCAGGTCTT
AGGAAAGAGAGGTACAAAATGAGAACAGAGAGAGAGCAGCACAGATGGGACTGTCAGGATTCAGACTCTTTCAGCCACCA
GTCAAAAGGGTGAAGTTACAGGAATCCATTGAATATGAAGACTTGGGGGGAAAGAATAGCATCAAAACTATTGCACTAAG
CCTAAAGAAGTCAGATCGGTATTATCATGGTCCAACAGCAATTCAGTCTCTCCAATGTGCAACAAGTCAGGATATTATCA
ATTGTTTTCAGACTATTAAGCAAGAGATGGAAACTTATACCCCCAGACTAACTCAGGTTCTTTCAAGTGGTGCTGCAAGT
AGTCCCATCATGGCCCTATCTCCTGAAGGAGCACTTATGCAGGGAGGGCCACAATAAGCCATAAACCAGATGGTGCCAAA
TGATAGTCAGTCAGAACTCAAACACTTGTATGTGGCTGTGGCAGAGCTGCTGAGGCATTTCTGGTCCTGTTTTCCAGTTA
ACACACCATTCCTAGAGGAAAAGGTAGTCAGGATGAAGAATAATTTGGAATGATTCCAAGCTATCAAGCTCTGCCCATTC
CAAGAAAAATTCAGAGATAGTATTTAAGCACAAATTTGGTAAGTCATATAGAAGAGATGCTGCAGACAGCCTACAATAAA
CTCCACACCTGGCAGTCTAGGTGCTTGCTGAAGAAG

Alignment

ORF - retro_mdom_1210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.84 %
• Parental protein coverage: 99.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLH
          MATSSEEVLLIVKK..QKKQDGAL.LMAERIAWAPEGKDRFTIS..YADIKCQKISPE.KAKIQLQLVLH
Retrocopy MATSSEEVLLIVKKICQKKQDGALCLMAERIAWAPEGKDRFTISLLYADIKCQKISPE*KAKIQLQLVLH

Parental  AGDTTNFHFSNESTAIKERDAVKDLLQQLLPKFKRKANKELEEK-NRMLQEDPVLFQLYKDLVVSQVISA
          AGDTTNFHFSN.S.A.KERDAV.DLLQ.LL..FKRKA.KEL..K.NRMLQEDP.LFQLYKDLVVSQVISA
Retrocopy AGDTTNFHFSNDSAAVKERDAVIDLLQELLSRFKRKAKKELKKK>NRMLQEDPTLFQLYKDLVVSQVISA

Parental  EEFWANRLSMNTVDSPAASNHKQDVGISAAFLADVRPQTDGCNGLRYNLTSDIIESIFRTYPAVKMKYAE
          EEFWA..L...T.DSPAASNHKQDVGIS.AFLADV.PQTDGCN.LRYNLTSDII.SI.RTYP.VK.K.AE
Retrocopy EEFWASGLRADTMDSPAASNHKQDVGISSAFLADVCPQTDGCNSLRYNLTSDIIDSICRTYPIVKLKHAE

Parental  NVPHNMTEKEFWTRFFQSHYFHRDRLNTGSKDLFAECAKMDEKGLKTMVSLGVKNPLLDLTALEDKSLDE
          NVPHNMTEK.FW.RFFQSHYFHRD.LN.GS..LFAECAKMDEKGLKT.VSLGVKNPLL.LTALEDKSLDE
Retrocopy NVPHNMTEKVFWARFFQSHYFHRDQLNIGSQHLFAECAKMDEKGLKTVVSLGVKNPLLELTALEDKSLDE

Parental  GYGVSPVPSTSN-SSKSIKENSNAAIIKRFNHHSAMVLAAGLRKQ-EAQHDHNE-NNSTDGNSR-DSD-F
          GYGVSP.P.T.N.SSKS.KEN.NAAIIKRFNHH.AMVLAAGLRK..E.Q....E...STDG..R.DSD..
Retrocopy GYGVSPGPCTQN<SSKSMKENNNAAIIKRFNHHNAMVLAAGLRKE<EVQNENRE<ESSTDGTVR<DSD<L

Parental  FQPPVKRVKLQESIEYEDLGKNNNIKTIALSLKKSDRYYHGPTPIQSLQYATSQDIINSFQSIKQEMETY
          FQPPVKRVKLQESIEYEDLG..N.IKTIALSLKKSDRYYHGPT.IQSLQ.ATSQDIIN.FQ.IKQEMETY
Retrocopy FQPPVKRVKLQESIEYEDLGGKNSIKTIALSLKKSDRYYHGPTAIQSLQCATSQDIINCFQTIKQEMETY

Parental  TPKLTQVLSSGAASSTITALSPGGALMQGGPQQAINQMVPSDIQSELKHLYVAVGELLRHFWSCFPVNTP
          TP.LTQVLSSGAASS.I.ALSP.GALMQGGPQ.AINQMVP.D.QSELKHLYVAV.ELLRHFWSCFPVNTP
Retrocopy TPRLTQVLSSGAASSPIMALSPEGALMQGGPQ*AINQMVPNDSQSELKHLYVAVAELLRHFWSCFPVNTP

Parental  FLEEKVVRMKNNLERFQATKLCPFQE-KIRRQYLSTNLISHIEEMLQTAYNKLHTWQSRRLLKK
          FLEEKVVRMKNNLE.FQA.KLCPFQE.KI.R.YLSTNL.SHIEEMLQTAYNKLHTWQSR.LLKK
Retrocopy FLEEKVVRMKNNLE*FQAIKLCPFQE<KIQR*YLSTNLVSHIEEMLQTAYNKLHTWQSRCLLKK

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_1210 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1210 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110768	1 retrocopy	retro_hsap_1892,
Gorilla gorilla	ENSGGOG00000008405	1 retrocopy	retro_ggor_1385,
Monodelphis domestica	ENSMODG00000006540	1 retrocopy	retro_mdom_1210 ,
Nomascus leucogenys	ENSNLEG00000017760	1 retrocopy	retro_nleu_1473,
Otolemur garnettii	ENSOGAG00000000710	1 retrocopy	retro_ogar_338,
Pan troglodytes	ENSPTRG00000003420	1 retrocopy	retro_ptro_1269,