RetrogeneDB ID: retro_mdom_1502

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:43274089..43275133(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS6KB1
• Ensembl ID: ENSMODG00000014313
• Aliases: None
• Description: ribosomal protein S6 kinase, 70kDa, polypeptide 1 [Source:HGNC Symbol;Acc:10436]

Sequence

>retro_mdom_1502
GGAGAATTATTTATGCAGTTAGAAAGAGAGGGAATATTTATGGAAGATACAGCGTGCTTTTACTTGGCAGAAATCTCCAT
GGCTTTGGGGCATTTACATCAAAAAGGGATCATCTACAGAGACCTGAAGCCGGAAAATATCATGCTTAATCACCAAGGTC
ATGTGAAATTGACAGACTTTGGACTATGCAAAGAATCTATTCATGATGGAACAGTTACACACACGTTCTGTGGAACAATA
GAATACATGGCCCCTGAAATCTTGATGAGAAGTGGCCATAATCGTGCTGTGGACTGGTGGAGTTTGGGGGCATTAATGTA
TGACATGCTGACTGGAGCACCCCCATTTACTGGGGAGAACAGAAAGAAGACAATTGACAAAATTCTCAAATGTAAACTTA
ATTTGCCTCCCTACCTCACACAAGAAGCCAGAGATCTGCTTAAAAAGCTGCTAAAAAGAAATGCTGCTTCACGTCTTGGA
GCTGGTCCTGGGGATGCTGGAGAAGTTCAGGCTCATCCTTTCTTCAGACACATTAACTGGGAAGAACTTCTGGCTCGGAA
GGTGGAGCCCCCTTTTAAACCTCTTTTGCAATCTGAAGAGGATGTGAGCCAGTTTGATTCAAAGTTTACACGGCAGACAC
CTGTTGACAGCCCAGATGATTCAACTCTCAGTGAAAGTGCCAACCAGGTTTTTCTGGGTTTTACATATGTGGCTCCATCT
GTACTTGAAAGTGTGAAAGAGAAATTTTCATTTGAACCAAAAATCTGATCACCTCGAAGATTCATTGGCAGCCCTCGGAC
ACCTGTCAGCCCAGTCAAATTTTCTCCTGGGGATTTCTGGGGAAGAGGTGCTTCAGCCAGTGCAGCAACTACTCAGACAC
CTGTGGATTATCCCATGGAGACGAGTGGAATAGAACAAATGGATGTGACGGTGAGTGGAGAGGCATCAGCACCACTTCCA
ATCCGACAGCCTAACTCTGGGCCATACAAAAAACAAGCTTTTCCCATGATTTCCAAACGGCCAGAACACTTGCGTATGAA
TCTA

Alignment

ORF - retro_mdom_1502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.71 %
• Parental protein coverage: 66.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GELFMQLEREGIFMEDTACFYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHDG
          GELFMQLEREGIFMEDTACFYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHDG
Retrocopy GELFMQLEREGIFMEDTACFYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHDG

Parental  TVTHTFCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCKLNLPPYLT
          TVTHTFCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCKLNLPPYLT
Retrocopy TVTHTFCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCKLNLPPYLT

Parental  QEARDLLKKLLKRNAASRLGAGPGDAGEVQAHPFFRHINWEELLARKVEPPFKPLLQSEEDVSQFDSKFT
          QEARDLLKKLLKRNAASRLGAGPGDAGEVQAHPFFRHINWEELLARKVEPPFKPLLQSEEDVSQFDSKFT
Retrocopy QEARDLLKKLLKRNAASRLGAGPGDAGEVQAHPFFRHINWEELLARKVEPPFKPLLQSEEDVSQFDSKFT

Parental  RQTPVDSPDDSTLSESANQVFLGFTYVAPSVLESVKEKFSFEPKIRSPRRFIGSPRTPVSPVKFSPGDFW
          RQTPVDSPDDSTLSESANQVFLGFTYVAPSVLESVKEKFSFEPKI.SPRRFIGSPRTPVSPVKFSPGDFW
Retrocopy RQTPVDSPDDSTLSESANQVFLGFTYVAPSVLESVKEKFSFEPKI*SPRRFIGSPRTPVSPVKFSPGDFW

Parental  GRGASASAATTQTPVDYPMETSGIEQMDVTVSGEASAPLPIRQPNSGPYKKQAFPMISKRPEHLRMNL
          GRGASASAATTQTPVDYPMETSGIEQMDVTVSGEASAPLPIRQPNSGPYKKQAFPMISKRPEHLRMNL
Retrocopy GRGASASAATTQTPVDYPMETSGIEQMDVTVSGEASAPLPIRQPNSGPYKKQAFPMISKRPEHLRMNL

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_1502 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1502 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
Canis familiaris	ENSCAFG00000017679	1 retrocopy	retro_cfam_771,
Monodelphis domestica	ENSMODG00000001260	1 retrocopy	retro_mdom_1083,
Monodelphis domestica	ENSMODG00000014313	2 retrocopies	retro_mdom_1502 , retro_mdom_819,