RetrogeneDB ID: retro_mdom_1791

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:122249658..122251203(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_mdom_1791
ATGAATGTTCCTGCAAGTAGTTGTGGAAGTCCCAGTTCTGCAGAAACAGTCAGTGACTTTAAAGATCTCTGGGCAAAACT
GAAGGAATGTCATGACAAAGAAGTACAAGCCTTACAGATCAAAGTAACCAAGCTGAAAAAAGAACGGATTTTAGATGCAC
AAAGATTGGAAGAGTTTTTTACTAAAAATCAACAACCGAGAGAGCAACAGAAAGCTCTTCATGACACCATTAAAGTTTTT
GAAGATCGGTTAAGAGCAGGATTGTGTGACCATTATGCAGTGACTGAAGAACACATGAGGAAAAAACAACAAGAATTTGA
AAATATTCAGCAACAAAATCTTAAACTGATCACTGAACTTATGAATGATAAGAATGCCTTACAAGAAGAAAACAAAAACT
TTCAGAGCAACTACATCAGAAACTTGAAAAGAAACGGCATCAAGTAGCAGAGCCTGTGGAGGAAATTATTCCTGATTCAC
CTATATTGACTTTCTCATTTCCTGGTCTTAACCAACTATGAAGAAAGAAGGAGAACCCACACATCCGGTATATAGAGCAA
GCAAATACTGATTTGGAGCACCCTCTGTGTACAAATGAATTTGCAAAAGGTCTAAAGTATTCAACTCAACTGCAGGAAAA
CCATTATGAAAATGAAATTCCTGTAGCAGACACTTGTGATCAAACATTATCAACTATGACCAATACCCAAGAAACCAATA
ATTATCCCATTGAAAAGCCATCTTTTAATTTAGCTGCTGTTGTTGCTGAAACACTCGGATTTGGTGTTCAAGAAGAATAT
GACTCTCAAAATGCTTTGAATTCTCTCAATGAAGACCTGCATCATCAGCAGTAAGCAGAGCTAAAGAAACAAACCTTTCA
AGAAGCCACAAAAAATATTGAAGATGGTTTAAGATTTTCAGATTCTTCTCCAAGGACTCCATCAGAAGTTGACTGGATTG
CTCGGGCATCTTCTCCTGTTTTTGGGGCTGCTTCTACTCTGAAAAATGGCTTAAGCACAAGCTTGTCCCCTTCTCTTTTA
GAGGCTGGAAAAAAGTTGCATCTCAAAACAAACCATTTCAGCAATAATTGTAATTCTAGGCCACAAAAACCTAGATCAAA
ATCTGAAGACACCAGCCTTGTTACATGCCTTAATCTTGGTTCTCAAGCAAGCACTGTTATTGATCATTCTTCTTCCATTA
AACAAGCATTTGTGAGAAATAATATAGATGAATCAATAAGTACAAAAGTTGGAACTGATACAAAAGATGAAGCTATTGGA
AAAAGTGATTGTTTTATGCCATTGAAACCATTGGGAGGCAGAGGAACCAAAAGAAAGAAAACTGAAGAATAAACTGAACA
TTGCCTCCAAACCTCTTTTGATAAAGAAAATGCTTTTCCTTTCTGGGGGGGATAGTTATCCTTCTGTCAATGGAGACTCT
TTCATGGATAAGCCCCTGGATCTATCTGATAGATTTTCAGCTATCCACCATCAAGAAAAAAGCCAAGGAAATGAGGTTAC
TGATGGTTATGAGCCAATAAAAATG

Alignment

ORF - retro_mdom_1791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.68 %
• Parental protein coverage: 57.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNVPASSCGSPSSAETVSDFKDLWAKLKECHDKEVQALQIKVTKLKKERILDAQRLEEFFTKNQQLREQQ
          MNVPASSCGSPSSAETVSDFKDLWAKLKECHDKEVQALQIKVTKLKKERILDAQRLEEFFTKNQQ.REQQ
Retrocopy MNVPASSCGSPSSAETVSDFKDLWAKLKECHDKEVQALQIKVTKLKKERILDAQRLEEFFTKNQQPREQQ

Parental  KALHDTIKVLEDRLRAGLCDRCAVTEEHMRKKQQEFENIRQQNLKLITELMNDKNALQEENK-KLSEQLH
          KALHDTIKV.EDRLRAGLCD..AVTEEHMRKKQQEFENI.QQNLKLITELMNDKNALQEENK.KLSEQLH
Retrocopy KALHDTIKVFEDRLRAGLCDHYAVTEEHMRKKQQEFENIQQQNLKLITELMNDKNALQEENK<KLSEQLH

Parental  QKIEKKRHQVAEPEEEIIPDSPILTFSFPGLNRLRRKKENPHVRYIEQANTDLEHPLCTNEFAKGLKCST
          QK.EKKRHQVAEP.EEIIPDSPILTFSFPGLN.L.RKKENPH.RYIEQANTDLEHPLCTNEFAKGLK.ST
Retrocopy QKLEKKRHQVAEPVEEIIPDSPILTFSFPGLNQL*RKKENPHIRYIEQANTDLEHPLCTNEFAKGLKYST

Parental  QLQQNHYENEILVADTCDQTLSTMTNTQETNNYPIEKSSFNLAAVVAETLGLGVQEESDSQNALNSLNED
          QLQ.NHYENEI.VADTCDQTLSTMTNTQETNNYPIEK.SFNLAAVVAETLG.GVQEE.DSQNALNSLNED
Retrocopy QLQENHYENEIPVADTCDQTLSTMTNTQETNNYPIEKPSFNLAAVVAETLGFGVQEEYDSQNALNSLNED

Parental  LHQQQEAEPKKQTFQEPTKNIEDGLRFSDSSPRTPPEVDWIARASSPVFGAASTLKNGLSTSLSPSLLEV
          LH.QQ.AE.KKQTFQE.TKNIEDGLRFSDSSPRTP.EVDWIARASSPVFGAASTLKNGLSTSLSPSLLE.
Retrocopy LHHQQ*AELKKQTFQEATKNIEDGLRFSDSSPRTPSEVDWIARASSPVFGAASTLKNGLSTSLSPSLLEA

Parental  GKKSHLKTNHFSNNCTSRPQKPRSKSEDTSLVTCLNLGSQASTVIDHSSSIKQVFVRKNIDESISTKIGT
          GKK.HLKTNHFSNNC.SRPQKPRSKSEDTSLVTCLNLGSQASTVIDHSSSIKQ.FVR.NIDESISTK.GT
Retrocopy GKKLHLKTNHFSNNCNSRPQKPRSKSEDTSLVTCLNLGSQASTVIDHSSSIKQAFVRNNIDESISTKVGT

Parental  DTKDEAIEKSDCFMPLKPLGGRGTKRKKTEEETEHCLQTSFDKENAFPF-RGDSYPSVNGDSVMDKPLDL
          DTKDEAI.KSDCFMPLKPLGGRGTKRKKTEE.TEHCLQTSFDKENAFPF..GDSYPSVNGDS.MDKPLDL
Retrocopy DTKDEAIGKSDCFMPLKPLGGRGTKRKKTEE*TEHCLQTSFDKENAFPF>GGDSYPSVNGDSFMDKPLDL

Parental  SDRFSAIHRQEKSQGNEVKKQFRQVAL
          SDRFSAIH.QEKSQGNEV.........
Retrocopy SDRFSAIHHQEKSQGNEVTDGYEPIKM

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_1791 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1791 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,