RetrogeneDB ID: retro_mdom_1200

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:459481573..459481950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KNSTRN
• Ensembl ID: ENSMODG00000000464
• Aliases: None
• Description: kinetochore-localized astrin/SPAG5 binding protein [Source:HGNC Symbol;Acc:30767]

Sequence

>retro_mdom_1200
GAGACTCATTCTCAGATTGCTTCTGAGAATATGATACACCAAAGGTCCAAAGAGGTAGAATGACACAAAGCTCTTACTTA
ACTCAACAGTCCCAAAGAATGAATTGTACAGAACTACTGAGGCAGATGAAGACTATGGATCCTGCTGCTAAGAAGATGAT
TAAAAAGAGCTCCAGCCCATTAAAATGACACAAAGTAGAGGAAGAGCTTCAAGAGAAGAATCAGCTGTTAGAGGCAATTA
ACAAGCAGTTGCATTTGAAGCTGACTGAAAGCCAGGGAGAGCTGAAGGTGCTCACTCAAAAAATGGAGTTCCTGGAGAAA
TTTCAGGATATCTACTTGGCAATTTTGGAGAGTGGTAATATTGGTCCAGTTACAGGA

Alignment

ORF - retro_mdom_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.93 %
• Parental protein coverage: 59.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETQSRTAFKSQIPQRSKEMELHKALN-STDPENELNKTTRQRQMKTMDPA-KKNIRKSYRPLSRQKAEEE
          ET.S..A....I.QRSKE.E.HKAL...T......N.T...RQMKTMDPA.KK.I.KS..PL...K.EEE
Retrocopy ETHSQIASENMIHQRSKEVE*HKALT<LTQQSQRMNCTELLRQMKTMDPAAKKMIKKSSSPLK*HKVEEE

Parental  LKEKNQLLEAVNKQLYLKLTESQEELKVLTQKVELLEESQDSYLAILESGNIDPVTG
          L.EKNQLLEA.NKQL.LKLTESQ.ELKVLTQK.E.LE..QD.YLAILESGNI.PVTG
Retrocopy LQEKNQLLEAINKQLHLKLTESQGELKVLTQKMEFLEKFQDIYLAILESGNIGPVTG

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	27.77 RPM
SRP007412_cerebellum	0.00 RPM	41.13 RPM
SRP007412_heart	0.00 RPM	8.77 RPM
SRP007412_kidney	0.00 RPM	17.12 RPM
SRP007412_liver	0.00 RPM	5.03 RPM
SRP007412_testis	0.00 RPM	347.49 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1200 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1200 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032340	2 retrocopies	retro_btau_1217, retro_btau_274,
Choloepus hoffmanni	ENSCHOG00000007085	3 retrocopies	retro_chof_1378, retro_chof_2237, retro_chof_504,
Monodelphis domestica	ENSMODG00000000464	1 retrocopy	retro_mdom_1200 ,
Otolemur garnettii	ENSOGAG00000009825	1 retrocopy	retro_ogar_1829,
Tupaia belangeri	ENSTBEG00000012043	4 retrocopies	retro_tbel_2696, retro_tbel_3958, retro_tbel_4092, retro_tbel_787,
Tursiops truncatus	ENSTTRG00000010577	1 retrocopy	retro_ttru_240,