RetrogeneDB ID: retro_mdom_5

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:68181814..68183023(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005047
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF7
• Ensembl ID: ENSMODG00000009994
• Aliases: None
• Description: DDB1 and CUL4 associated factor 7 [Source:HGNC Symbol;Acc:30915]

Sequence

>retro_mdom_5
ATGGCCCAGGTATCCCGAACCGATTATCAGTACCGCAAGATCTACAGGTATGAAGCCCCATGGACTGTGTATGCCATGAA
TTGGAGCGTACGGGCCGACCAGCCCTTCCGCTTGGCTCTGGGAAGTTTTATGGAAGAATACGGTAACAAGGTACAACTCG
TGAGCCTGGCCTCTGACTGGGTTGACACCCACGGGGACTTTATATGTGGCCACACTCTGAACCACCCGTATCCCGCTACC
AAGGTTATGTGGATCCCTGACCCTCAGGGTATTCGTCCAGACCTACTAGCCACTAGCGGCGACTACCTACGGGTGTGGCG
CTGCCCAAGTGCCACTGAGGTGCTTCCTGCCACGGGTAGAGCGAGGGGAACTATCCATGGCGCCCAGGCAGCAGGGGGCA
GTGTTTTCCAAGGGCGCGGGCGTGGCCGAGGGCGCGGTCGCGGTCGCGGGCGCGGTTTCACTGTTGCCGAGGCTGCTTCC
ACAGTTGGGGCAGCCGCTGATTTGGAACCCCGCCTCGAATGCCTCCTTAATCACAACAAGAATACCCGCTTCTGCTCTCC
CCTCACCTCTTTTGATTGGAACGAGACAGACCCCTCCCTTCTGGCCACGTCAAGCAGCGACACGACTTGCACCATCTGGG
CCCTGGAGACCCGCCAGATAGTGGGCCGAGTGTCCGGGCATGGGAAGTCGCAGATTGTTAACCATGACAAAGAGGTCTAT
GACGTTGCCTTCGGAGGGGGCCGAGATGTGTTCGCTTCGGTGGGTGCTGATGGCTCCTTGCGTATGTTTGACCTGCGCCA
GCTGGACCGCAACACCGTGGTGTATGAGGAACCCCAGCGCCTGCCACTGCTGCGCCTTGCCTGGAACAAAAAAGACCTTA
ACTACGTAGCCACCGCAGCCATGAATTCCACTGAGGTAGTCATTCTCGACCTGCGTATGCCTGGCCAGCCTGTGGTCCAC
CTCAACCGCCACGGAGCCTGCGTCAACGGGATTACCTGGGCGCCTCACTCTTCGGGCCACATCTGCACTGCTGCCGACGA
CCACCGCGCTCTCATCTGGGACTTTCAGCAGAACCCCCCAGCTGCTGAGGACCCCATTCTGACCTACACCGCCAATGGGG
AGATTAACAACGTGCAGTGGGCCTCCGCCAATCACCCTGACTGGATTGCCATCTGCTACAAAAACTTTCTGGAACTGCTC
CGGGTCTAA

Alignment

ORF - retro_mdom_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.45 %
• Parental protein coverage: 71.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VWRVGETETRLECLLNNNKNSDFCAPLTSFDWNEVDPYLLGTSSIDTTCTIWGLETGQVLGRVNLVSGHV
          V......E.RLECLLN.NKN..FC.PLTSFDWNE.DP.LL.TSS.DTTCTIW.LET.Q..GR...VSGH.
Retrocopy VGAAADLEPRLECLLNHNKNTRFCSPLTSFDWNETDPSLLATSSSDTTCTIWALETRQIVGR---VSGHG

Parental  KTQLIAHDKEVYDIAFSRAGGGRDMFASVGADGSVRMFDLRHLEHSTIIYEDPQHHPLLRLCWNKQDPNY
          K.Q...HDKEVYD.AF...GGGRD.FASVGADGS.RMFDLR.L...T..YE.PQ..PLLRL.WNK.D.NY
Retrocopy KSQIVNHDKEVYDVAF---GGGRDVFASVGADGSLRMFDLRQLDRNTVVYEEPQRLPLLRLAWNKKDLNY

Parental  LATMAMDGMEVVILDVRVPCTPVARLNNHRACVNGIAWAPHSSCHICTAADDHQALIWDIQQMPRAIEDP
          .AT.AM...EVVILD.R.P..PV..LN.H.ACVNGI.WAPHSS.HICTAADDH.ALIWD.QQ.P.A.EDP
Retrocopy VATAAMNSTEVVILDLRMPGQPVVHLNRHGACVNGITWAPHSSGHICTAADDHRALIWDFQQNPPAAEDP

Parental  ILAYTAEGEINNVQWAS-TQPDWIAICYNNCLEILRV
          IL.YTA.GEINNVQWAS...PDWIAICY.N.LE.LRV
Retrocopy ILTYTANGEINNVQWASANHPDWIAICYKNFLELLRV

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_5 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_5 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001071	1 retrocopy	retro_dnov_2453,
Monodelphis domestica	ENSMODG00000009994	1 retrocopy	retro_mdom_5 ,