RetrogeneDB ID: retro_mdom_249

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:158885081..158886401(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024587
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000000967
• Aliases: None
• Description: None

Sequence

>retro_mdom_249
ATGAAAAAATTCTTCCAAGAGATCAAGGCGGACATCAAGTTCAAGAGCGCTGGGCCCGGGCAGAAACTCACGGACACGGC
GGGGGAAAAGGGCTCCAAGGAACGACAGAGCCAACAAGCAAGCAAGCAACCCCGCCAGGACCCTACCAATGAAGCCCAAA
TGGCAGCAGCGGCGGCACTGGCCAGGCTGGAACAGAAACAACCACGGTCTCGAGGACCCACATCCCAAGATTCCATCCGG
AACCAAGTGAAGAAGGAATTACAAGCAGAAGTCACTGTTAGTGGTATCTCTGAGTCTTCTGGAGCAAATGTGATACCTGA
GGCTAAGGAGGAGGGCTCTGCAAACCTGTCGGTGACTGGGGTTTATTTTACCTGCCCATTTACTGGAGCCATCTTGAGAA
AGGACCAGAGGGATGCCCACATCAAAGAGGTCATTAATGAGTATGCGGACAAAGACCCAGTGACTGCTTCCATCATGAAG
ATCCATACGTTCAACAGGGACCGAGAGAAAGTGAAGTCGGGGGTGGACACCATTGCCAAGTACCTGGACAACATCCATCT
TCACCCAGAAGAGGAGAAATACAGGAAAATCAAATTGCAAAACAAAGTGTTTCAAGAGCGGATCAACTGCCTAGAAAGGG
CTAATGAATTTTTCAGGGCCATTGGGTTTGAGAAGACGTCTCTCCCTGTTCCAGAACAAGAGGCCTTGGAAGAATTCTAT
GTGCTGGGGGAGGATGCCCAAGTAGAGAAGCTAGAACAGCACAAAGTCGCTCTGCAGAACTCAGAACCAGTGCGGGCTCA
GCTGGCCCGGCAGCGACGAATCTTCAAGCCCTCCCCTTTGGCTGCCCAGTTTGACCTACCTGGGGACTTCTTCAACCTCA
CGACTGAGGAGCTCAAACGGGAGCAGAAACTAAGGACGGACCCTGTGGAACGGCTGTCTGTGCTTCGGACCAAAGCCATG
CGGGAGAAGGAGGAGCAGAGGGAAATGAGAAAATATACCTATACCCTCTTACAGGTCCGCTTTCCAGATGGGCACATCCT
CCAGGGTACCTTCTATGCTCGGGAGCGGCTGTCTGCACTCTACAGCTATGTGAGGGAGGCACTGCAAAGTGACTGGCTGC
CCTTTGAACTGATTCCTGTAGGCGGGCACAAACTGTTGGACAACAGCTTAGCCTTCAACGAATGTGGGCTGGTGCCTTCA
GCTCTTCTAACTTTCACTTGGGATGCAGCCGTCATGGACGACATCAAGGCATCAGGGGCCGAACAGCCCCCAGGAGCTCT
CAAACCTGAACTTCTTGCTACTGTGGAAAGCCTCTCATGA

Alignment

ORF - retro_mdom_249 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKKFFQEIKADIKFKSAGPGQKLTDTAGEKGSKERQSQQASKQPRQGPTNEAQMAAAAALARLEQKQPRS
          MKKFFQEIKADIKFKSAGPGQKLTDTAGEKGSKERQSQQASKQPRQ.PTNEAQMAAAAALARLEQKQPRS
Retrocopy MKKFFQEIKADIKFKSAGPGQKLTDTAGEKGSKERQSQQASKQPRQDPTNEAQMAAAAALARLEQKQPRS

Parental  RGPTSQDSIRNQVKKELQAEATVSGISESSGANVIPEAKEEGSANLSVTGVYFTCPFTGAILRKDQRDAH
          RGPTSQDSIRNQVKKELQAE.TVSGISESSGANVIPEAKEEGSANLSVTGVYFTCPFTGAILRKDQRDAH
Retrocopy RGPTSQDSIRNQVKKELQAEVTVSGISESSGANVIPEAKEEGSANLSVTGVYFTCPFTGAILRKDQRDAH

Parental  IKEVINEYADKDPVTASIMKIHTFNRDREKVKLGVDTIAKYLDNIHLHPEEEKYRKIKLQNKVFQERINC
          IKEVINEYADKDPVTASIMKIHTFNRDREKVK.GVDTIAKYLDNIHLHPEEEKYRKIKLQNKVFQERINC
Retrocopy IKEVINEYADKDPVTASIMKIHTFNRDREKVKSGVDTIAKYLDNIHLHPEEEKYRKIKLQNKVFQERINC

Parental  LEGANEFFRAIGFEKTSLPVPEQEALEEFYVLGEDAQVEKLEQHKVALQNSEPVRAQLARQRRIFKPSPL
          LE.ANEFFRAIGFEKTSLPVPEQEALEEFYVLGEDAQVEKLEQHKVALQNSEPVRAQLARQRRIFKPSPL
Retrocopy LERANEFFRAIGFEKTSLPVPEQEALEEFYVLGEDAQVEKLEQHKVALQNSEPVRAQLARQRRIFKPSPL

Parental  AAQFDLPGDFFNLTTEELKREQKLRTDAVERLSVLRTKAMREKEEQREMRKYTYTLLRVRFPDGHILQGT
          AAQFDLPGDFFNLTTEELKREQKLRTD.VERLSVLRTKAMREKEEQREMRKYTYTLL.VRFPDGHILQGT
Retrocopy AAQFDLPGDFFNLTTEELKREQKLRTDPVERLSVLRTKAMREKEEQREMRKYTYTLLQVRFPDGHILQGT

Parental  FYARERLSALYSYVREALQSDWLPFELIPVGGHKLLDDSLAFNECGLVPSALLTFTWDAAVMDDIKASGA
          FYARERLSALYSYVREALQSDWLPFELIPVGGHKLLD.SLAFNECGLVPSALLTFTWDAAVMDDIKASGA
Retrocopy FYARERLSALYSYVREALQSDWLPFELIPVGGHKLLDNSLAFNECGLVPSALLTFTWDAAVMDDIKASGA

Parental  EQPPGALKPELLATVESLS
          EQPPGALKPELLATVESLS
Retrocopy EQPPGALKPELLATVESLS

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_249 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_249 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000000967	1 retrocopy	retro_mdom_249 ,
Mustela putorius furo	ENSMPUG00000005027	1 retrocopy	retro_mputfur_1648,
Sarcophilus harrisii	ENSSHAG00000000301	1 retrocopy	retro_shar_551,