RetrogeneDB ID: retro_mdom_445

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:577498541..577500077(+)
• Located in intron of: ENSMODG00000010328

Retrocopy information

• Ensembl ID: ENSMODG00000010333
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000021493
• Aliases: None
• Description: None

Sequence

>retro_mdom_445
ATGATTGTTCCTGCAAGTAGTTGTAGAAGTCTCAGTTCTGCAGAAACAGTCAGTGACTTCAAAGATCTCTGGGCAAAACT
GAAGGAATGTCATGACAAAGAAGTACAAGCCTTACAGATCAAAGTAACCAAGCTGAAAAAGGAACAGATTTTAGATGCAC
AAAGATTGGAAGTGTTTTTTACTAAAAATCAACAACTGAGAGAGCAACAGAAAGCTCTTCATGACACCATTAAAGTTTTG
GAAGATCGGTTAAGAAGAGCAGGGTTGTGTGACCGTTGTGCAGTGACTGAAGAACACATGAAGAAAAAACAAGAATTTGA
AAATATTCGGCAACAAAATCTTACTGAACTTATGAATGATAAGAATGCCTTACAAGAAGAAAACAAAAAACTTTCAAAGC
AACTACATCAGAAAATTGAAAAGAAACGGCATCAAGTAGCAGAGCCTGAGGAGGAAATTATTCCTGATTCACCTATATTG
ACTTTCTCATTTCCTGGTCTTAACCGACTACGAAGAAAGAAGGAGAACCCACACGTCCAATATATAGAGCAAGCAAATAC
TGATTTGGAGCACCCTCTGTGTACAAACGAATTTGCAAAAGGTCTAAAGTGTTCGACTCAACTGCAGCAAAAGCACTATG
AAAATGAAATTCTTGTAGCAGACACTTGTGATCAAACATTATCAACTATGACCAATACCCAAGAAACCAACAATTATCCC
ATTGAAAAGTCATCTTTTAATTTAGCTGCTGTTGTTGCTGAAACACTCGGACTTGGTGTTCAAGAAGAATCTGACTCTCA
AAATGCTTTGAATTCCCTCAATGAAAACCTGCATCATCAGCAGGAAGCAGAGCCAAAGAAACAAACCTTTCAAGAACCCA
CAAAAAATATCGAAGATAGTTTAAGATTTTCAGATTCTTCTCCAAGGACTCCACCAGAAGTTGACTGGATTGCTCGGGCA
TCTTCTCCTGTTTTGGGGGCTGCTTCTACTCTGAAAAATGGCTTAAGCACAAGCTTGTCCCCTTCTCTTTTAGAGGCTGG
AAAAAAGTCGCATCTCAAAACAAAGCATTTCAGCAATAATTGTAATTCTAGGCCACAAAAACCTAGATCAAAATCTGAAG
ACACCAGCCTTGTTACATGCCTTAATCTTGGTTCTCAAGCAAGCACTGTTATTGATCATTCTTCTTCCATTAAACAAGTA
TTTGTGAGAAAGAATATAGATGAATCAATAAGTACAAAAGTTGGAATTGATACAAAAGATGAAGCTATTGAAAAAAGTGA
TTGTTTTATGCCATTGAAACCATTGGGAGGCAGAGGAACCAAAAGAAAGAAGACTGAAGAAGAAACTGAACATTGCCTCC
AAACCTCTTTTGATAAAGAAAGTGCTTTTCCTTTCCGAGGGGATAGTTATCCTTCTGTCAATGGAGACTCTGTCATGGAT
AAGCCCCTGGATCTATCTGATAGATTTTCAGCTATCCACCGTCAAGAAAAAAGCCAAAGAAATGAGGTTACTGGTGGTTA
TGAGCCAATAAAAATG

Alignment

ORF - retro_mdom_445 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.41 %
• Parental protein coverage: 57.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNVPASSCGSPSSAETVSDFKDLWAKLKECHDKEVQALQIKVTKLKKERILDAQRLEEFFTKNQQLREQQ
          M.VPASSC.S.SSAETVSDFKDLWAKLKECHDKEVQALQIKVTKLKKE.ILDAQRLE.FFTKNQQLREQQ
Retrocopy MIVPASSCRSLSSAETVSDFKDLWAKLKECHDKEVQALQIKVTKLKKEQILDAQRLEVFFTKNQQLREQQ

Parental  KALHDTIKVLEDRLR-AGLCDRCAVTEEHMRKKQQEFENIRQQNLKLITELMNDKNALQEENKKLSEQLH
          KALHDTIKVLEDRLR.AGLCDRCAVTEEHM.KKQ.EFENIRQQNL...TELMNDKNALQEENKKLS.QLH
Retrocopy KALHDTIKVLEDRLRRAGLCDRCAVTEEHMKKKQ-EFENIRQQNL---TELMNDKNALQEENKKLSKQLH

Parental  QKIEKKRHQVAEPEEEIIPDSPILTFSFPGLNRLRRKKENPHVRYIEQANTDLEHPLCTNEFAKGLKCST
          QKIEKKRHQVAEPEEEIIPDSPILTFSFPGLNRLRRKKENPHV.YIEQANTDLEHPLCTNEFAKGLKCST
Retrocopy QKIEKKRHQVAEPEEEIIPDSPILTFSFPGLNRLRRKKENPHVQYIEQANTDLEHPLCTNEFAKGLKCST

Parental  QLQQNHYENEILVADTCDQTLSTMTNTQETNNYPIEKSSFNLAAVVAETLGLGVQEESDSQNALNSLNED
          QLQQ.HYENEILVADTCDQTLSTMTNTQETNNYPIEKSSFNLAAVVAETLGLGVQEESDSQNALNSLNE.
Retrocopy QLQQKHYENEILVADTCDQTLSTMTNTQETNNYPIEKSSFNLAAVVAETLGLGVQEESDSQNALNSLNEN

Parental  LHQQQEAEPKKQTFQEPTKNIEDGLRFSDSSPRTPPEVDWIARASSPVFGAASTLKNGLSTSLSPSLLEV
          LH.QQEAEPKKQTFQEPTKNIED.LRFSDSSPRTPPEVDWIARASSPV.GAASTLKNGLSTSLSPSLLE.
Retrocopy LHHQQEAEPKKQTFQEPTKNIEDSLRFSDSSPRTPPEVDWIARASSPVLGAASTLKNGLSTSLSPSLLEA

Parental  GKKSHLKTNHFSNNCTSRPQKPRSKSEDTSLVTCLNLGSQASTVIDHSSSIKQVFVRKNIDESISTKIGT
          GKKSHLKT.HFSNNC.SRPQKPRSKSEDTSLVTCLNLGSQASTVIDHSSSIKQVFVRKNIDESISTK.G.
Retrocopy GKKSHLKTKHFSNNCNSRPQKPRSKSEDTSLVTCLNLGSQASTVIDHSSSIKQVFVRKNIDESISTKVGI

Parental  DTKDEAIEKSDCFMPLKPLGGRGTKRKKTEEETEHCLQTSFDKENAFPFRGDSYPSVNGDSVMDKPLDLS
          DTKDEAIEKSDCFMPLKPLGGRGTKRKKTEEETEHCLQTSFDKE.AFPFRGDSYPSVNGDSVMDKPLDLS
Retrocopy DTKDEAIEKSDCFMPLKPLGGRGTKRKKTEEETEHCLQTSFDKESAFPFRGDSYPSVNGDSVMDKPLDLS

Parental  DRFSAIHRQEKSQGNEVKKQFRQVAL
          DRFSAIHRQEKSQ.NEV.........
Retrocopy DRFSAIHRQEKSQRNEVTGGYEPIKM

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	0.50 RPM	0.00 RPM
SRP007412_testis	0.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_445 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_445 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000021493	2 retrocopies	retro_mdom_1791, retro_mdom_445 ,
Oryctolagus cuniculus	ENSOCUG00000007333	1 retrocopy	retro_ocun_1145,
Tursiops truncatus	ENSTTRG00000009810	1 retrocopy	retro_ttru_1575,