RetrogeneDB ID: retro_mdom_1449

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:93668916..93670857(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H11A
• Ensembl ID: ENSMODG00000001184
• Aliases: None
• Description: zinc finger CCCH-type containing 11A [Source:HGNC Symbol;Acc:29093]

Sequence

>retro_mdom_1449
CAGGGACGCTATGTTGAAAGCCTTTTCCTACCTCCAAGCAAAACTATTTTACCCCTTGTGCCTGAGTTGCCAGATGAAGA
GGTGAAATCTAGTCAGCTCTCAATGCATCAGAACAAACTGTCTGTTCAGTCCAATCCCTCTCCCCAGCTTCAAGGGGTAA
TGAAAGTGGAAAGTTCAGAAAATGTCCCCAGCCCCACACATCCTCCAGTTGTAATCAATGCTGCAGATGATGATGAGGAT
GACGATGATCAGTTTTCTGAAGAAGGAGATGAAACTAAAACACCTATTCTGCAACCAGCTCCTGAAGTTCATAATGGATT
ACGCATAACTGGTGCTCGGAAGCCAGGGGTCAACTTAAAGCAAGGAGATAGTTTGAATTTTGGAATAAAACCCTTGAAGA
AATCAAATCAAAGAAAATGAAGGAAAAATCTAAGAAGCAAGGAGAAGCGCCTTCAGGAGCATGTGCTCATTTACTTCGAC
CTCAACACATTCCAGGTCCTGAGAAAGAGAATGTCAGAACTGTGGTGAGGACAGTAACCCTGTCCAACAAACAAGAAGAG
CCCTTGGTATGATTCAGTCTCACAGAAAGACTAGGGAAATGGAAACTCTCAGGTGTTGACAGTGACCCTCCACTGAAGCG
AAGCCTTGCTCAAAGGCTTGGGATGAAAAATGAGTCTCCAAAAATCATTACTGACAAAACACCAAAGAAAGTTCAAGTTT
CCAAGCCTCTGAAGGAGAGATTAGGAATGCCAGCTGATCTAAACAGTATGGAGACAACAGCAGAAAGATCTGCTAAAGGT
AGACAGATCCATGTAAAGACACTAGAAGAAATACGTCTTGAGAGAGCCAGCCAAAAACGAGGAGAATTGCTAACCAAAAT
CAAGAATGAAGGACCCCATAAGCCTCAAGATTCCAGTTTGGGGATGAGGAGCTCCTCTGCTATCCGAATCAAAACATTTT
CTGAGGTCCTGGCTGAAAAGAAACGCCGACAGCAGGAAGAAGAGAGACAGAAAGCTGAGAAGGAAAACCCTTCTGTCAAG
CTCAGAATAGAGAGTGAGTCTAAGAAACCAGCTGTCTTGCCTCCCAGCACTACCAGCAAAGGGCAGCTGGAAGAGCCTGC
AATGAAAACCAAGCCCATGCAGGAGGTACACATAAAAACCTTGGAGGAAATCAAACAGGAAAAAGCATTGAGAGTGCAAC
AGAGTGCTGAGAACAGCACCAGCTCCCAGAAACAGCCTGAGACTACTCCAATCATAAGACGACTCCTCTGCATCACCAGA
AGAACAGGTGTAAAGGAAGAGAAGAAACTTAGTGAAGCAGGTGAAGCCACATCTCGAATTGGTGTTAGCAGAACAGAGGC
TGTTGAGGTTTCTTCACAGACTTCTGATGAGACCACAGGAGATAGCATTTCCAAAGTTCAAGTCAAGAAATTCGAGGATA
TCATGAGAAAGAAGCACATGCAGAAGCAGCAAGAGGTAGAAATGCTACCAAAAGGAGAATGTTCTGACACCCCTTCAGGA
AGAAGCAGCACCCAGTAACACCCAAGTGGTAGAGAAATCAGAACTGAATACTGTATCAGGAATCACCCACCAGCTGACAA
AACGCATGCCAATAAAAGCCCAGCAAGTAGAGCTAGAAACTTCAGGAATTGGGGATTCAATCCTGAATGTGAAATGTGCA
GCACAACCCTTGGAAAAAAGGGGTAAAGCCAAGCCCAAGGTTAGTGTCAAGCCATCTGTGGTTAAAGTCATTTCAACCCC
TAAATTGGCCACAAAACCCAAAGCAGCTGAAGTCCACTCTGCTGTCATTGCAGCCATAAAACCACTTAGTTCCTGCAATA
TTCTTCAGGAAAGCCCAAGCAAAAAAGGAGCCCTGGCTGCTGTTCCAGTTCTCTCTGAGGATAAACCAGTCACTGTGTCT
GAGACAGAAAAAACTCCAAAC

Alignment

ORF - retro_mdom_1449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.23 %
• Parental protein coverage: 88.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RGRYVEGLFLPPSKTILPLVPESPDEEVKSSQLSMQQNKLSVQSNPSPQLRGVMKVESSENVPSPTHPPV
          .GRYVE.LFLPPSKTILPLVPE.PDEEVKSSQLSM.QNKLSVQSNPSPQL.GVMKVESSENVPSPTHPPV
Retrocopy QGRYVESLFLPPSKTILPLVPELPDEEVKSSQLSMHQNKLSVQSNPSPQLQGVMKVESSENVPSPTHPPV

Parental  VINAADDDEDDDDQFSEEGDETKTPILQPAPEVHNGLRITGARKPGVSLKQGDSLNFGIK-TLEEIKSKK
          VINAADDDEDDDDQFSEEGDETKTPILQPAPEVHNGLRITGARKPGV.LKQGDSLNFGIK.TLEEIKSKK
Retrocopy VINAADDDEDDDDQFSEEGDETKTPILQPAPEVHNGLRITGARKPGVNLKQGDSLNFGIK<TLEEIKSKK

Parental  MKEKSKKQGEGPSGACAHLLQPQPIPGPEKENVRTVVRTVTLSNKQGEEPLVRLSLTERLGKRKLSGVDS
          MKEKSKKQGE.PSGACAHLL.PQ.IPGPEKENVRTVVRTVTLSNKQ.EEPLV..SLTERLGK.KLSGVDS
Retrocopy MKEKSKKQGEAPSGACAHLLRPQHIPGPEKENVRTVVRTVTLSNKQ-EEPLV*FSLTERLGKWKLSGVDS

Parental  DPPLKRSLAQRLGKKIESPEMNTDKTPKKVQVSKSLKERLGMPADLNSMETT-ERSAKGGEIHVKTLEEI
          DPPLKRSLAQRLG.K.ESP...TDKTPKKVQVSK.LKERLGMPADLNSMETT.ERSAKG..IHVKTLEEI
Retrocopy DPPLKRSLAQRLGMKNESPKIITDKTPKKVQVSKPLKERLGMPADLNSMETTAERSAKGRQIHVKTLEEI

Parental  RLERASQKRGELLTKIKNEGPHKPEDSNLGMRSSSAIRIKTFSEVLAEKKHRQQEEERQKAEKENPSVKL
          RLERASQKRGELLTKIKNEGPHKP.DS.LGMRSSSAIRIKTFSEVLAEKK.RQQEEERQKAEKENPSVKL
Retrocopy RLERASQKRGELLTKIKNEGPHKPQDSSLGMRSSSAIRIKTFSEVLAEKKRRQQEEERQKAEKENPSVKL

Parental  RIESESKKPAILPPSTTSKGQLEEPAMKTKPMQEVHIKTLEEIKQEKALRVQQSAENSTSSQTQPETTPI
          RIESESKKPA.LPPSTTSKGQLEEPAMKTKPMQEVHIKTLEEIKQEKALRVQQSAENSTSSQ.QPETTPI
Retrocopy RIESESKKPAVLPPSTTSKGQLEEPAMKTKPMQEVHIKTLEEIKQEKALRVQQSAENSTSSQKQPETTPI

Parental  IRRLLRITKRTGVKEEKKLSEAGETTSRIGVSRTEAVEVSSQTSDETTGDSISKVQVKKFEDIMREKRMQ
          IRRLL.IT.RTGVKEEKKLSEAGE.TSRIGVSRTEAVEVSSQTSDETTGDSISKVQVKKFEDIMR.K.MQ
Retrocopy IRRLLCITRRTGVKEEKKLSEAGEATSRIGVSRTEAVEVSSQTSDETTGDSISKVQVKKFEDIMRKKHMQ

Parental  KQQEVEMLP-KDKVLTPLQEEAAPSNTQVVEKSELNTVSGITRQLTKRMPIKAQQVELETSGIGDSILNV
          KQQEVEMLP.K..VLTPLQEEAAPSNTQVVEKSELNTVSGIT.QLTKRMPIKAQQVELETSGIGDSILNV
Retrocopy KQQEVEMLP>KENVLTPLQEEAAPSNTQVVEKSELNTVSGITHQLTKRMPIKAQQVELETSGIGDSILNV

Parental  KCAAQPLEKRGKAKPKVNVKPSVVKVISTPKLATKRKAAEVHPAVIAAVKPLSSGNILQESPSKKAAVAA
          KCAAQPLEKRGKAKPKV.VKPSVVKVISTPKLATK.KAAEVH.AVIAA.KPLSS.NILQESPSKK.A.AA
Retrocopy KCAAQPLEKRGKAKPKVSVKPSVVKVISTPKLATKPKAAEVHSAVIAAIKPLSSCNILQESPSKKGALAA

Parental  VPVLSEDKPVTVSETEKTPN
          VPVLSEDKPVTVSETEKTPN
Retrocopy VPVLSEDKPVTVSETEKTPN

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_1449 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1449 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000058673	2 retrocopies	retro_hsap_3481, retro_hsap_508,
Monodelphis domestica	ENSMODG00000001184	1 retrocopy	retro_mdom_1449 ,
Mus musculus	ENSMUSG00000026464	2 retrocopies	retro_mmus_3323, retro_mmus_564,
Otolemur garnettii	ENSOGAG00000000243	1 retrocopy	retro_ogar_3250,
Pan troglodytes	ENSPTRG00000001876	5 retrocopies	retro_ptro_2980, retro_ptro_2981, retro_ptro_2991, retro_ptro_380, retro_ptro_382,
Rattus norvegicus	ENSRNOG00000002993	3 retrocopies	retro_rnor_1570, retro_rnor_1673, retro_rnor_602,