RetrogeneDB ID: retro_mdom_329

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:154363292..154364093(+)
• Located in intron of: ENSMODG00000009566

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002633
• Aliases: None
• Description: None

Sequence

>retro_mdom_329
GAAGACAACTGGGAAAAGAACTTAAAAAGCAAGATAAGTCATCTGGAAACAGAAAACAGTGTCTTGAAAGCCAAGATTAA
TCAACCTGAAAATGAGGCAACAAAGATGAAAGATGACCTCAAAAGAAAATCAGACCAGAAGGAAAAGGATGACCAAAAAG
CCAAGGATAAAATGCAGTCTTTAAAAACCAGAATACAACAATCAGAAGCAAATGACTTCACAAGGCAGCAGGACACTATA
AAACAAAATGAAAAGAATGAAAAAATTGAGGAAAATATGAAGTATCTCATTCACAAAACAGAAGATTTAGAAAATAGTTC
TACAAGAGATAAATTAAGAATCATTGGTCTACTGGAAGACCATGACAAAAGAAAATCCTGGACATGATACTACAGGAAAT
TATTCAAGAAAACTGCCCCGATATTCTAGGAAAAGAGGGAAAAGTGGAGACTGAAAGTCCCCAACTGACAACACTCAGGA
ATGTTATAGATAAATTCATGAACTATCAGACCAAGGAAAAAATATTACAAGATGCCAAGAAGAAGTCATTCAGATACCAT
GGAACCACAGTGAGGATAACACAGGATCTGGCTGCATCTACACTGAAAAGACCAAAAGTCATGGAATATGATATTCTGTA
AAGCAAGGGAACTAGGTCTACAACCAAAAATCAATTACCCAGCAAAATTGACTATAATCTTACAGAGGAAAGTATGGTCA
TCTAACAAAATACAATAATTGCAAGCATTTGTAAATAAAAGACCAGATGTGAACCTAAAATCTGATGCCCAAACACAGAA
C

Alignment

ORF - retro_mdom_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.57 %
• Parental protein coverage: 77.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDQTEKQKQS----LKTRIKQLEDKQEKHEKVNTKHRETEKRISDQKEKDDEKARDEIQSFKTRIQQLEA
          ED..EK...S....L.T....L..K....E...TK.....KR.SDQKEKDD.KA.D..QS.KTRIQQ.EA
Retrocopy EDNWEKNLKSKISHLETENSVLKAKINQPENEATKMKDDLKRKSDQKEKDDQKAKDKMQSLKTRIQQSEA

Parental  SDFTRHQHTIKQNQKNKIIEENMKHLIHKTEDLENRSRRDNLRIIGLLEDYDKRKS-LDIILQEIIQENC
          .DFTR.Q.T.............MK.LIHKTEDLEN.S.RD.LRIIGLLED.DKRKS.LD.ILQEIIQENC
Retrocopy NDFTRQQDTXXXXXXXXXXXXXMKYLIHKTEDLENSSTRDKLRIIGLLEDHDKRKS<LDMILQEIIQENC

Parental  PDITEQEGKVEIERIHRSTHRNVLAKFKKSQTKEKILQVDKKKSFRKHGTIVRITQDLTASTL-KDLQAW
          PDI...EGKVE.E.....T.RNV..KF...QTKEKILQ..KKKSFR.HGT.VRITQDL.ASTL.KD...W
Retrocopy PDILGKEGKVETESPQLTTLRNVIDKFMNYQTKEKILQDAKKKSFRYHGTTVRITQDLAASTL>KDQKSW

Parental  NMIFWKARELGLQPRIIYTAKLTIFLQGKVWSFNKIEDFQAFVKKRPDMNRKFDAEAQN
          NMIF.KARELGLQP.I.Y.AKLTI.LQ.KVWS.NKI...QAFV.KRPD.N.K.DA..QN
Retrocopy NMIFCKARELGLQPKINYPAKLTIILQRKVWSSNKIQ*LQAFVNKRPDVNLKSDAQTQN

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	0.24 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	0.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_329 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_329 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002633	6 retrocopies	retro_mdom_1009, retro_mdom_1362, retro_mdom_1477, retro_mdom_1723, retro_mdom_1764, retro_mdom_329 ,