RetrogeneDB ID: retro_meug_1801

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold59986:580..1921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFX5
• Ensembl ID: ENSMEUG00000011101
• Aliases: None
• Description: regulatory factor X, 5 (influences HLA class II expression) [Source:HGNC Symbol;Acc:9986]

Sequence

>retro_meug_1801
AAGCAGGATGTTTATGATGCTTATAGGAGGTACTGTGAGAGCTTAGCCTGCTACCGCCCACTCAGCACTGCCAACTTTGG
CAAAATCATCCAAGAAATCTTCCCTGGCATCAAGCCCTGGAGTCTGGGAGGCTGGGGCCAATCCAAAGGTTGCTATGGTG
GTATTTGAGGAAAGACCCTGGTATCTATGCTACCCTTGCCTGGACTCGACCTCAAAGGCTCAGAGAGTCCAGAGTTGGGC
CCAGAAGTGGGTCCAGGTCCTTGGGATGAACTAGTGGAAGCAGCCTGTGCCCTAACCTGTGGCTAGGAAGAGCGGATATT
AAAATGCTCCTTCAGGTCCATCATCGAGGTAGCCCAGTGTCTGCTGCAGCAACATCTCCCCTCTGCTCAATCTGCTCGTG
CACATCTGCTCATGGCCATGATGCTCGCTGAGGAACCTGAAGGGCTCCCATGGGATCCCACTACCAAGAATGGTGTGGAG
AGCCCAGAAGGAAGAGCCTCTACAAGTCAGTCCCAGCCCCTCAAGGAGCTGGAGTCCTGAACTAGGTCTGCCGCCCCAGT
TTGAGGGGAGTGAAAGAAAACTGCAGAAACCTCAGCCCCAGCCGCCACCAGCCCCCAAGTGAAAGCTCTGGTTGCCTGCC
TGTGCTCCTCCCCCGGGTACCCCAACCACAACTCCAAGTCTTCCCACTAGTCCTAGCCCCCAAACTTCCCTCAGGTACCC
TAAAAGTCACTATACTGCCTTTGTCCAGTGGGGCTGGGGTATCCCAGGGAGCTCTGCCCATCATCAACATGATCTTGCCC
ATTGTATCTGCTGTGCCTATACCTGGGAGAGCTCCATTGGAAGGTCCCATCCAGTCACAGGGCCTTGAGAAAAACAGGGA
GATAGGTCCAAGGGTGGACACGGGACCATGGGGCAAGGGAGTAAAGAGGACAGCTGAAGTGCCTAGGAGTGACAACAAGG
GACAATAGCTAGCAGCCAAAGTATTAAGCCAGGATACAGAAGAGATAGGGATTGATGCCAAGCATAAAAGAGGGTGTCCT
CAAAAGAAATCAAATGATGAGGATGAACAGAGCTCATCCACTGAGAAGCCACTGCCTGCTACAGACTCTGCCCATTCCCC
TAGGGTACCACAGGACTCTTGGGGCTTTGGAGGGGAGAGTGACCTGGCAAGAGGGTCAGTGAAAAAAAGTGGAGGAGAAA
AAAGTGCCTTCCCTTGGCCAGGAAGACAGCACTGATTTCAAGGGAGGAAGGGGAAGAAGTGCCCAACATGCCAAAGAAAC
AGGGGACAAAAGTCTTGTCACTCCTAAAGTGAGTGTCATTAAGGGCAACAGGAGCTGGGAT

Alignment

ORF - retro_meug_1801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 74.96 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KQDVYDAYRRYCESLACCRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKTLVSMPPLPGLD
          KQDVYDAYRRYCESLAC.RPLSTANFGKII.EIFP.IK...LGG.GQSK.CY.GI..KTLVSM.PLPGLD
Retrocopy KQDVYDAYRRYCESLACYRPLSTANFGKIIQEIFPGIKPWSLGGWGQSKGCYGGI*GKTLVSMLPLPGLD

Parental  LKGSESPELGPEVGPGPRDELVEAACALTCDWAERILKRSFSSIVEVARFLLQQHLISARSAHAHLLMAM
          LKGSESPELGPEVGPGP.DELVEAACALTC...ERILK.SF.SI.EVA..LLQQHL.SA.SA.AHLLMAM
Retrocopy LKGSESPELGPEVGPGPWDELVEAACALTCG*EERILKCSFRSIIEVAQCLLQQHLPSAQSARAHLLMAM

Parental  VLADEPEA-PSKGATKNGVENPEGRVSKNQPQPPKELEPRTGSAAPVRGE-RKKTAKTSAPATSSPQVNA
          .LA.EPE..P....TKNGVE.PEGR.S..Q.QP.KELE..T.SAAPV.GE..K.......P....P....
Retrocopy MLAEEPEGLPWDPTTKNGVESPEGRASTSQSQPLKELES*TRSAAPV*GE<VKENCRNLSPSRHQPPSES

Parental  LVARLPVLLPRVPQPQLPRPVRVSPPVLAPKLPSATLKVTTLPLSSGAGVSQGALPIINMILPTVSAVPI
          ....LPVLLPRVPQPQL.....V.P.VLAPKLPS.TLKVT.LPLSSGAGVSQGALPIINMILP.VSAVPI
Retrocopy SGC-LPVLLPRVPQPQL----QVFPLVLAPKLPSGTLKVTILPLSSGAGVSQGALPIINMILPIVSAVPI

Parental  PGRAPLEGPTQSQGLEKNREIGPGVDVGPRGKGVKRTAEVPMSDTRGQELAAKVLSQDTEEIGIDAKRKR
          PGRAPLEGP.QSQGLEKNREIGP.VD.GP.GKGVKRTAEVP.SD..GQ.LAAKVLSQDTEEIGIDAK.KR
Retrocopy PGRAPLEGPIQSQGLEKNREIGPRVDTGPWGKGVKRTAEVPRSDNKGQ*LAAKVLSQDTEEIGIDAKHKR

Parental  GRPRKKSNGEGEQSSSTEKPLPATDSAHSLRVPQESWGF--ESDLARGSV-GKVEEKKVPSLGQEDSTDF
          G.P.KKSN.E.EQSSSTEKPLPATDSAHS.RVPQ.SWGF..ESDLARGSV..KVEEKKVPSLGQEDSTDF
Retrocopy GCPQKKSNDEDEQSSSTEKPLPATDSAHSPRVPQDSWGFGGESDLARGSV>KKVEEKKVPSLGQEDSTDF

Parental  KGGRGSSAQHAKETGDKSLVAPKVSVIKGNRNWE
          KGGRG.SAQHAKETGDKSLV.PKVSVIKGNR.W.
Retrocopy KGGRGRSAQHAKETGDKSLVTPKVSVIKGNRSWD

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_1801 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1801 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000011101	1 retrocopy	retro_meug_1801 ,