RetrogeneDB ID: retro_mdom_563

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:319716882..319718163(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000013066
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBBP4
• Ensembl ID: ENSMODG00000017415
• Aliases: None
• Description: retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]

Sequence

>retro_mdom_563
ATGGCCGACAAGGAAGCAGCCCTTGATGATGCTGTAGAAGAACAGGTGAGCAATGAGAAATATAAAATATGGAAAAAAAA
TACTCCTTTCCTCTATGACTTAGTGATGACCCATGCCCTAGAATGTCCCAGCCTGACTGCACAGTGGCTTCCAGATGTAA
CAAGACCCGAAGGGAAAGATTTCAGCATTCATCGACTTGTGCTGGGTACACACACATCCGATGTGCAGAATCATCTTGTG
ATAGCCAGTGTGCAGCTCCCCAATGATGATGCTCAGTTTGATGCCTCTCCCTATGACAGTGAGAAAGGGGAATTTGGAGG
CTTTGGCTCAGTTAGCGGGAAAATTAAAATTGAAATCAAGATTAACCATGAGGGAGAAGTGAACAGGGCCCGTTATATGC
CTCAGAATCCTTGCATCATTGCAACAAAGACTCCATCCAGTGATGTCCTTGTTTTTGACTACACCAAGCACCCTTCAAAG
CCAGACCCTTCTGGGAAGTGTAACCCAGACTTGCGCCTCGGTGGACATCAAAAGGAGGGCTATGGCTTGTCGTGGAACCC
AAATCTCAGTGGATACTTGCTTAGTGCATCAGATAACCACACCATCTGCTTGTGGGACATCAGTGCTGTTCCAAAGGAAG
GCAAAGTGGTGGATGCAAAGACCATATTCACGAGACACACAGAGGTAGTCGAAGACGTTTCTTGGCACCTCCTCCACGAA
TCTCTCTTTGGATCAGTTGCGGATGATCAGAAGCTTATGATCTGGGACACGCGGTCAAACAATACTTCTAAACCAAGCCA
CTTAGTGGATGCCCACACTGCTGAAGTAAATTGTATTTCTTTTAATCCTTATAACGAGTTCATTCTCGCCACAGGATCAG
CTGATAAGACAGTTGCATTGTGGGATCTTAGAAATCTGAAATTGAAGCTGCATTCCTTTGAGTCACATAAGGATGAAATA
TTGGAGGTTCAGTGGTCTCCTCACAATGAAACTATCTTGGCTTCTAGTGGCACTGACCCAAGGCTGAACATCTGGGACTT
GAGTAAAATTGGGGAGGAGCAGTCCCCAGAAGATGCAGAAGATGGCCCACCAGAATTGTTGTTTATTCATGGTGGCCACA
CTGCCAAAATATCTGATTTCTCCTGGAACCCAAATGAACCTTGGGTTATTTGTTCTGTATCAGAAGACAATATCATGCAA
ATCTGGCAGATGGCTGAGAACATACACAATGATGAAGACCCTGAAGGAAGTGTGGATCCAGATCCAGAGGGACAGGGGTC
C

Alignment

ORF - retro_mdom_563 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGT
          MADKEAA.DDAVEE.V.NE.YKIW...TPFLYDLVMTHALE.PSLTAQWLPDVTRPEGKDFSIHRLVLGT
Retrocopy MADKEAALDDAVEEQVSNEKYKIWXXXTPFLYDLVMTHALECPSLTAQWLPDVTRPEGKDFSIHRLVLGT

Parental  HTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCII
          HTSD.QNHLVIASVQLPNDDAQFDAS.YDSEKGEFGGFGSVSGKI.IEIKINHEGEVNRARYMPQNPCII
Retrocopy HTSDVQNHLVIASVQLPNDDAQFDASPYDSEKGEFGGFGSVSGKIKIEIKINHEGEVNRARYMPQNPCII

Parental  ATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAV
          ATKTPSSDVLVFDYTKHPSKPDPSG.CNPDLRL.GHQKEGYGLSWNPNLSG.LLSASD.HTICLWDISAV
Retrocopy ATKTPSSDVLVFDYTKHPSKPDPSGKCNPDLRLGGHQKEGYGLSWNPNLSGYLLSASDNHTICLWDISAV

Parental  PKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLS
          PKEGKVVDAKTIFT.HT.VVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSH.VDAHTAEVNC.S
Retrocopy PKEGKVVDAKTIFTRHTEVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHLVDAHTAEVNCIS

Parental  FNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKI
          FNPY.EFILATGSADKTVALWDLRNLKLKLHSFESHKDEI..VQWSPHNETILASSGTD.RLN.WDLSKI
Retrocopy FNPYNEFILATGSADKTVALWDLRNLKLKLHSFESHKDEILEVQWSPHNETILASSGTDPRLNIWDLSKI

Parental  GEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSV--
          GEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQ.WQMAENI.NDEDPEGSV..
Retrocopy GEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQIWQMAENIHNDEDPEGSVDP

Parental  DPEGQGS
          DPEGQGS
Retrocopy DPEGQGS

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	0.33 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.50 RPM	0.00 RPM
SRP007412_testis	248.49 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_563 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_563 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 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001021	7 retrocopies	retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus	ENSCPOG00000015352	3 retrocopies	retro_cpor_154, retro_cpor_27, retro_cpor_899,
Macaca mulatta	ENSMMUG00000009940	1 retrocopy	retro_mmul_75,
Monodelphis domestica	ENSMODG00000017415	6 retrocopies	retro_mdom_1542, retro_mdom_1833, retro_mdom_1873, retro_mdom_1900, retro_mdom_563 , retro_mdom_765,
Mustela putorius furo	ENSMPUG00000015214	1 retrocopy	retro_mputfur_104,
Procavia capensis	ENSPCAG00000011030	1 retrocopy	retro_pcap_116,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Rattus norvegicus	ENSRNOG00000021492	1 retrocopy	retro_rnor_1270,
Sarcophilus harrisii	ENSSHAG00000010923	1 retrocopy	retro_shar_399,