RetrogeneDB ID: retro_mdom_1747

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:186169753..186170721(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BZW1
• Ensembl ID: ENSMODG00000015000
• Aliases: None
• Description: basic leucine zipper and W2 domains 1 [Source:HGNC Symbol;Acc:18380]

Sequence

>retro_mdom_1747
GTATTTGCAGCACAAGAAGACCTAGAGACCATGCAAGCCTTTGCTCAGGTATTCAACAACTTAATCAGGCGATACAAATA
CCTTGAAAAGGGATTTGAGGATGAAGTTAAAAAGCTGCTGCTATTCTTAAAGGGTTTTTCAGAGTCTAAGAGGAACAAAC
TAGCCATGCTGACTGGGTTCTTCTGGCCAATGGGACACTTAATGCATCCATTCTTAACAGCCTTTATAATGACAATTTGG
TTAAAGAAGGCATTTCAGCAGCCTTTGCTGTAAAGCTGTTTAAATCATAGATAAATGAAAAAGATATCAATGCAGTAGCT
GCTAGTCTTCAAAAAGTCAGCATGGACAACAGACTGATGGAACTTTTTCTGGCCAACAAGCAAAGTGTTGAGCACTTCAC
AAAATATTTTACCGAAGCAGGTCTAAAAGAACTTTCTGAGTATGTTCGGAACCAGCACACCATAGGAGCTCGTAAAGAGC
TACAGAAAGAACTGCAAGAACAAATGTCACGTGGTGATCCATTTAAGGATGTAATTTTGTATGTCAAGGAGGAGATGAAG
AAAAACAGTATCCCAGAACAGATCGTTATAGGCATAGGCTTGTCAAGTGTAATGAGCACTGTGGAATGGAACAAAAAGGA
GGAGCTGGTGGCAGAGCAAGCCATCAAGCATTTGAAGCAATAGAGCCCTCTACTTGCTGCCTTTACTACTCAAGGTCAGT
CTGAGCTGACCCTGTTACTGAAGATTCAGGAGTACTGTTATGACAACATTCACTTCATGAAAGCCTTCCAGAAAATCGTG
GTGCTTTTTTCTAAAGCTGAAGTCCTGAGTGAAGAGCCCATTTTGAAGTGGTATAAAGATGCACATGTTGCAAAGGGGGA
AAGTGTCTTCCTTGAGCAAATGAAAAAATGTATAGAGTGGCTCAAGAATGCAGAAGAAGAATCTGAGTCTGAAGCGGAAG
AAGGCGAC

Alignment

ORF - retro_mdom_1747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.44 %
• Parental protein coverage: 77.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFAAQEDLETMQAFAQVFNKLIRRYKYLEKGFEDEVKKLLLFLKGFSESERNKLAMLTG-VLLANGTLNA
          VFAAQEDLETMQAFAQVFN.LIRRYKYLEKGFEDEVKKLLLFLKGFSES.RNKLAMLTG.VLLANGTLNA
Retrocopy VFAAQEDLETMQAFAQVFNNLIRRYKYLEKGFEDEVKKLLLFLKGFSESKRNKLAMLTG<VLLANGTLNA

Parental  SILNSLYNENLVKEGVSAAFAVKLFKSWINEKDINAVAASLRKVSMDNRLMELFPANKQSVEHFTKYFTE
          SILNSLYN.NLVKEG.SAAFAVKLFKS.INEKDINAVAASL.KVSMDNRLMELF.ANKQSVEHFTKYFTE
Retrocopy SILNSLYNDNLVKEGISAAFAVKLFKS*INEKDINAVAASLQKVSMDNRLMELFLANKQSVEHFTKYFTE

Parental  AGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYVKEEMKKNNIPEQIVIGIVWSSVMSTVE
          AGLKELSEYVRNQ.TIGARKELQKELQEQMSRGDPFKD.ILYVKEEMKKN.IPEQIVIGI..SSVMSTVE
Retrocopy AGLKELSEYVRNQHTIGARKELQKELQEQMSRGDPFKDVILYVKEEMKKNSIPEQIVIGIGLSSVMSTVE

Parental  WNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQEYCYDNIHFMKAFQKIVVLFYKAEVLSEE
          WNKKEELVAEQAIKHLKQ.SPLLAAFTTQGQSELTLLLKIQEYCYDNIHFMKAFQKIVVLF.KAEVLSEE
Retrocopy WNKKEELVAEQAIKHLKQ*SPLLAAFTTQGQSELTLLLKIQEYCYDNIHFMKAFQKIVVLFSKAEVLSEE

Parental  PILKWYKDAHVAKGKSVFLEQMKKFVEWLKNAEEESESEAEEGD
          PILKWYKDAHVAKG.SVFLEQMKK..EWLKNAEEESESEAEEGD
Retrocopy PILKWYKDAHVAKGESVFLEQMKKCIEWLKNAEEESESEAEEGD

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_1747 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1747 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 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003543	8 retrocopies	retro_chof_1519, retro_chof_2060, retro_chof_2092, retro_chof_2451, retro_chof_2517, retro_chof_689, retro_chof_726, retro_chof_838,
Microcebus murinus	ENSMICG00000003355	1 retrocopy	retro_mmur_831,
Monodelphis domestica	ENSMODG00000015000	1 retrocopy	retro_mdom_1747 ,
Tarsius syrichta	ENSTSYG00000013638	2 retrocopies	retro_tsyr_2177, retro_tsyr_483,
Tursiops truncatus	ENSTTRG00000003639	1 retrocopy	retro_ttru_153,