RetrogeneDB ID: retro_meug_1849

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold65342:6267..6828(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDKN3
• Ensembl ID: ENSMEUG00000002497
• Aliases: None
• Description: cyclin-dependent kinase inhibitor 3 [Source:HGNC Symbol;Acc:1791]

Sequence

>retro_meug_1849
AATAAACAGACTTCATTTCAGTTATCATAGCTAACCTTTTGCCTTGTTCATTGTTCTCAGTTTCTAGGTTTATGTTCTTT
TCCGGGTTGTAAATTCAAAGATGTTAGGAGAAATCTTCAAAAGGACATGGAAGAACTAAAGAAATATGTTATGCAAGATA
TATTTGTGTTCTGTTCCAGAGGAGAGCTGTCAAAATATCGAATACCAAACCTTTTAGATTTCTTTCAGCAGCCTGAAATT
ATCACTTACCACCATCTTATCCCAGATGGAGATGCCCTGACATAGACCTATGTTGTGGAATCCTGCAGGACCTTGCAGTC
TGTCTGGAAAACAATCAGAAAACCTTAAAACATTGTTATGGAGGACTTGAGTCATCTAGTCTTGTAGCAGCTTGCCTCCT
ATTACACTTACATGATCTAGTATCACTGATGCAGGCAATTGACAACCTTTGAAATTTAAACAGATCTGGGGTCATACAGA
CCATAAAACAATTATCTCTATGATGTTTGAGACAAACTTGCTGCACATCTGTCAACAAGAAACTTTGTATCAAGATCTGT
A

Alignment

ORF - retro_meug_1849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.97 %
• Parental protein coverage: 90.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NEQTPFQVSWLPLSLVNCSQFLGLCSLPXXXXXXXXXXXXXXXXELKNYGIQDIFVFCTRGELSKYRVPN
          N.QT.FQ.S.L...LV.CSQFLGLCS.P................ELK.Y..QDIFVFC.RGELSKYR.PN
Retrocopy NKQTSFQLS*LTFCLVHCSQFLGLCSFPGCKFKDVRRNLQKDMEELKKYVMQDIFVFCSRGELSKYRIPN

Parental  LLDFYQQHGIIIHHHPIPDGDT-PDIDRCCGILQELAVCLENNRKTLIHCYGGLGRSCLVAACLLLYLSD
          LLDF.QQ..II..HH.IPDGD..PDID.CCGILQ.LAVCLENN.KTL.HCYGGL..S.LVAACLLL.L.D
Retrocopy LLDFFQQPEIITYHHLIPDGDA<PDIDLCCGILQDLAVCLENNQKTLKHCYGGLESSSLVAACLLLHLHD

Parental  TVSPQQAIDSLRDLRGSGAIQTIKQ-YNYLHDFRDKLAAHLSARDSVSRSV
          .VS..QAID.L..L..SG.IQTIKQ.Y.Y..D..DKLAAHLS.R..VSRSV
Retrocopy LVSLMQAIDNL*NLNRSGVIQTIKQ>YLY--DV*DKLAAHLSTRNFVSRSV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1849 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1849 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012823	1 retrocopy	retro_chof_1806,
Echinops telfairi	ENSETEG00000018617	1 retrocopy	retro_etel_1763,
Felis catus	ENSFCAG00000015089	2 retrocopies	retro_fcat_135, retro_fcat_626,
Loxodonta africana	ENSLAFG00000014833	1 retrocopy	retro_lafr_637,
Macropus eugenii	ENSMEUG00000002497	3 retrocopies	retro_meug_1255, retro_meug_1768, retro_meug_1849 ,
Procavia capensis	ENSPCAG00000015559	1 retrocopy	retro_pcap_104,
Sarcophilus harrisii	ENSSHAG00000008977	1 retrocopy	retro_shar_502,
Tupaia belangeri	ENSTBEG00000010203	2 retrocopies	retro_tbel_1809, retro_tbel_4700,