RetrogeneDB ID: retro_mdom_1898

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:20322826..20323265(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT7
• Ensembl ID: ENSMODG00000019055
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 7 [Source:HGNC Symbol;Acc:14101]

Sequence

>retro_mdom_1898
AAAATAAATATGAGTAAACAACAGGAGAAAAAGAAGGAAGTTATGATTGAAACTTCTTTGGGGATAAAGAACAAAGAACA
GTGATATTGGTACAGTGTATTTTGAAGAAATGCTCATGATATTGGGCATTGTGCTATGTGGGGGGTTCAAATGACTTTCA
TTTCACAGTGGCTATGATGTTGGCTATTTGATCAAAATCCTGACCAACTCTAACCTACTTGAAGAAAAGCTGGACTTCTT
TGAGATCCTGAGATTGTTCTCCCTGGTTATCTAGGATGTCAAGTACCTCATGAAAAGCTGCAAGAACCTCAAGTGTAGAC
CACAGGGAGTGGCTGAGCAGCTTGAGTTGGAGCAGATAGGCCCATAGTACCAGGCAGGTTCTGATTTCTTACTGCCAGGA
ATGACCTTTTTCAAAATGACTGAAATGTTCTTTGAAGAT

Alignment

ORF - retro_mdom_1898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.33 %
• Parental protein coverage: 52.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KFNLTEDMYAQDSIELLTTSGIQFKKHEEE-GIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKI
          K.N..............T..GI...K..E...I.T.YF.E.LM..G.VLC.G.K.LSFHSGYD.GYLIKI
Retrocopy KINMSKQQEKKKEVMIETSLGI---KNKEQ>DIGTVYFEEMLMILGIVLCGGFK*LSFHSGYDVGYLIKI

Parental  LTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAF
          LTNSNL.EE.LDFFEILRLF..VI.DVKYLMKSCKNLK...Q.VAEQLELE.IGP..QAGSD.LL.GM.F
Retrocopy LTNSNLLEEKLDFFEILRLFSLVI*DVKYLMKSCKNLKCRPQGVAEQLELEQIGP*YQAGSDFLLPGMTF

Parental  FKMREMFFED
          FKM.EMFFED
Retrocopy FKMTEMFFED

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_1898 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1898 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
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Gorilla gorilla	ENSGGOG00000015762	2 retrocopies	retro_ggor_282, retro_ggor_3027,
Monodelphis domestica	ENSMODG00000019055	2 retrocopies	retro_mdom_1898 , retro_mdom_802,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,