RetrogeneDB ID: retro_mdom_853

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:206272694..206273564(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002698
• Aliases: None
• Description: None

Sequence

>retro_mdom_853
TGGAAGATACAATTCAAAACACAATTAAGAGAGGCTGAAGATAACTGGGAAAAGAATTTAAAAAGCAAGATAAGTCTAGA
TAGAAACAGAGGCACTTGAACTAAAATGAGAATATTGTGTCTTGAAAGCCAAAATTAATCAGCTTGAAAATGAGGCAAAT
GAGATGAAAGATGAGGCAAAGATGATGAAAGATGACCTCCAAAGAAAATCAGACCAGAAGGAGAAGGATGACCAAAAAGC
TAGGGATGAAATTCAAGCCTTAAAAACCAGAATACAACAATTAGAAGCAAGCAGTCTCACAAGGCAGCAGGAAACTATAA
AACAAAACCAAAAGAATGAAAAAATTGAGGAAAATATGAAACATCTCATTCACAAAACAGAAGATCTAGAAAATTGTTCC
AGAAGAGACAACTTAAGAATAATTGGTCTACCAGAAGGCCATAACAAAAGAAAAAGTGTGTACATCATCCTACAGCAAAT
TATCCAAGAAAACTGCCCCGACATTCTAGAACAAGAGGGAAAAGTGGAGATTGAAGGAATCCACAGATCAACTCCTGTAC
TTAATCCCCAACTGACAACACCCAGGAATGTTATAGGCAAATTCAAGAACTACCACACCAAGGAAAAAAATTACAAGCTG
ATAAGAAGAAATCATTCAGATACCATTCAGACACCAGATACCAGATACTATTCAGAACAGTGAAGATAACACAGGATCTG
GCTGCATCTATACTGAAGGACCAAAAGGCATGGAATATGATATTCCAGAAAGCAAGGGAACTAGGTCTATAACCAAGAAT
CAACTACCCAGCAAAACTGACTATATTCTTACAGGGGAAAGTATGGTCATTTAATAAAATAGAAGAATTC

Alignment

ORF - retro_mdom_853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.82 %
• Parental protein coverage: 82.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WEKNLKTKISHLETE-NSVLKAKTNQ-IENEAKEMKYEEKKMKDEARKMKDEAKEMRDEVKRMKDDLQRK
          W....KT.....E......LK.K....IE.EA.E.K.E....K.......................LQRK
Retrocopy WKIQFKTQLREAEDNWEKNLKSKISL>IETEALELK*EYCVLKAKINQXXXXXXXXXXXXXXXXXXLQRK

Parental  SDQKEKDDQKARDEIQSLRTRIQQLELSDLTRQQDTIKQNQKNEKIEDNMKHLIHKTEDLENLLRRDNLR
          SDQKEKDDQKARDEIQ.L.TRIQQLE.S.LTRQQ..................LIHKTEDLEN..RRDNLR
Retrocopy SDQKEKDDQKARDEIQALKTRIQQLEASSLTRQQXXXXXXXXXXXXXXXXXXLIHKTEDLENCSRRDNLR

Parental  ITGLPEDNDKRKSLDKILKEIIQENCLGIQEQEGKVKPERMHRSPSVLNPKLTTPRNGIAKFKNYQNKE-
          I.GLPE...KRKS...IL..IIQENC..I.EQEGKV..E..HRS..VLNP.LTTPRN.I.KFKNY..KE.
Retrocopy IIGLPEGHNKRKSVYIILQQIIQENCPDILEQEGKVEIEGIHRSTPVLNPQLTTPRNVIGKFKNYHTKE<

Parental  KILQAAKKKR-RMTKKARDEIQVR---ITQDMAASTLKDRKTWNIILRKAREQCLQRRINYPAKLIIFLE
          K.LQA.KKK..R.....R..I..R...ITQD.AAS.LKD.K.WN.I..KARE..L..RINYPAKL.IFL.
Retrocopy KKLQADKKKSFRYHSDTRYQILFRTVKITQDLAASILKDQKAWNMIFQKARELGL*PRINYPAKLTIFLQ

Parental  GKVWLFNKIEEF
          GKVW.FNKIEEF
Retrocopy GKVWSFNKIEEF

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_853 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_853 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002698	1 retrocopy	retro_mdom_853 ,
Monodelphis domestica	ENSMODG00000014482	1 retrocopy	retro_mdom_1991,