RetrogeneDB ID: retro_meug_1862

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold6678:1463..2462(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSTF3
• Ensembl ID: ENSMEUG00000005640
• Aliases: None
• Description: cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa [Source:HGNC Symbol;Acc:2485]

Sequence

>retro_meug_1862
CTCAAAACTAAAAATTATGAGGAGGTTGAAAAGTTATTTCAGAGATGTCTTTTAAAGGTTTTAAATATTGATTTGTGGAA
GTGTTATCTTTCATATATCAGAGAAAACAAGACAAAACTACCCAATTACAAAGAAAAATTGGCACAAGCATATGACTTTT
CTTTGAGTAAAATTGGAATGGAAGTTACATCTTTTCCGATTTGGATGGATTACATTAATTTCTTGAAAGGCATGGAAGCT
GATGGATGTTATGCAGAAAATCAAAGAATAGCAGCTGTCCGACGAGTTTATCAACGAGGTTGTGTTAATCCAATGGTCAA
TATTGAGTACCTTTGGTGGGATTACAGAAGATATGAAGAGGGCATCAACATGTATCTAGCTAAAAAAATGATTGAAGATA
GGAGAAAAAATTACATGAATGCGAGACGTGTAGCAAAGGAGTATGAAACAGTAATGAAAGGTTTAGACCGCAGTGCCCCT
CCAGTACGTCCACAGAATACTCTCCAAGAGGCTCAGCAAGTAGGCATGTGGAAGAACTATATACGGTGGGAAAAGAACAA
CCCTCTCCAAACCGAAGACCAGGGGCTCATAATAAAAAGAGTTATTTTTGCATATGAGCAGTGCCTGCTAGTGCTGGGCC
ATCACCCAGATATTTGGTATGAAGCTGCCCAGTACCTGGAGCAGGCCAGTAAGCTGCTAGCTGAGAAAGGGGACACTATT
CATGCTAAATTATTTAGCGATGAAACTGCTAAGATATATGAGAGAGCTATTAGCACTTTAATGAAAAAAAATATGCTTCT
TTATTTTGCATATGCAGATTATGAAGAGGGTAGAATGAAATTTGAGAAGGTACATGGCATATACAATAGACTCCTGGCAA
TTAGGGATATTGACCCTACTCTGGTATATATCCAGTATATGAAGTTTGCAAGGCGAGCAGAAGGCATCAAATCTGGAAGG
ATGGTATTTAAAAAAGCAAGACAGGANNNNNNNNNNCGA

Alignment

ORF - retro_meug_1862 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.48 %
• Parental protein coverage: 63.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IKAKNYDKVEKLFQRCLMNVLHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVD
          .K.KNY..VEKLFQRCL..VL.IDLWKCYLSY.RE.K.KLP.YKEK.AQAYDF.L.KIGME..S..IW.D
Retrocopy LKTKNYEEVEKLFQRCLLKVLNIDLWKCYLSYIRENKTKLPNYKEKLAQAYDFSLSKIGMEVTSFPIWMD

Parental  YINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEGINIHLAKKMIEDRSRDYMN
          YINFLKG.EA.G.YAENQRI.AVRRVYQRGCVNPM.NIE.LW.DY..YEEGIN..LAKKMIEDR...YMN
Retrocopy YINFLKGMEADGCYAENQRIAAVRRVYQRGCVNPMVNIEYLWWDYRRYEEGINMYLAKKMIEDRRKNYMN

Parental  ARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLL
          ARRVAKEYETVMKGLDR.AP.V.PQNT.QEAQQV.MWK.YI.WEK.NPL.TEDQ.LI.KRV.FAYEQCLL
Retrocopy ARRVAKEYETVMKGLDRSAPPVRPQNTLQEAQQVGMWKNYIRWEKNNPLQTEDQGLIIKRVIFAYEQCLL

Parental  VLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMK
          VLGHHPDIWYEAAQYLEQ.SKLLAEKGD...AKLFSDE.A.IYERAISTL....MLLYFAYADYEE.RMK
Retrocopy VLGHHPDIWYEAAQYLEQASKLLAEKGDTIHAKLFSDETAKIYERAISTLMXXXMLLYFAYADYEEGRMK

Parental  YEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDTRTR
          .EKVH.IYNRLLAI.DIDPTLVYIQYMKFARRAEGIKSGRM.FKKAR.....R
Retrocopy FEKVHGIYNRLLAIRDIDPTLVYIQYMKFARRAEGIKSGRMVFKKARQXXXXR

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_1862 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1862 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000005640	1 retrocopy	retro_meug_1862 ,
Myotis lucifugus	ENSMLUG00000003073	1 retrocopy	retro_mluc_240,
Monodelphis domestica	ENSMODG00000009745	1 retrocopy	retro_mdom_1,