RetrogeneDB ID: retro_meug_555

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold13599:18847..20521(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMEUG00000000475
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX1
• Ensembl ID: ENSMEUG00000008254
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 1 [Source:HGNC Symbol;Acc:2734]

Sequence

>retro_meug_555
ATGGGTGTGATGCCCGAGAATGCGCAGGCCATGGAGGAGATGGACTGGTTCCTCCCGACGGACATCAGGCCGAGTCCATC
CTGCTGATCCTGGGAGGAGGGGACGTGCTCATGGCTGCAGAAACAGGAAGTGGAAAGACTGGTGCCTTCAGTATCCCGGT
TATCCAGATAGTTTATGAGACCCTGAAGGACCAGCAGGAGGGCAAGAAAGGGAAGACCACTGTGAAAACTGGGGCTGCAG
TGCTCAACAAATGGCAGATGAACCCATATGACAAAGGGTCTGCTTTTGCAATTGGGTCAGACGGTCTTTGCTGCCAAAGC
CGAGAAGTGAAGGAATGGCATGGGTGTCGGTCAACGAAAGGAGTGATGAAAGGAAAACACAACTATGAAGTGTCCTGTCA
CGACCAAGGCTTGTGCAGAGTTGGGTGGTCCACTTCCCAGGCTTCCCTAGATTTGGGTACCGATAAGTTTGGCTTTGGCT
TTGGTGGAACTGGAAAGAAGTCCCATAACAAACAGTTTGACAATTATGGAGAGGAATTCACTATGCATGATACAATTGGA
TGTTACCTGGATGTTGACAAAGGCCAGGTTAAGTTCTCAAAAAATGGAAAAGACCTTGGTCTAGCTTTCAAAATACCAGC
CCACCTGAAGAACCAGGCATTCTTTGCTGCATGTGTCTTAAAGAATGCTGAACTGAAATTTAACTTTGGTGAAGAAGAAT
TTAAATTTCCCCCCAAAGACGGATTTGTTGGTCTCTGCAAGGCTTCTGATGGCCATGTAGTGAAATCTCAACACACAGGA
AGTGCACAGGTGGCGCAGACCAAGTTTCTTCCCAATGCTCCCAAGGCCCTTATTGTGGAGCCATCCCGGGAGCTGGCAGA
GCAGACTTTGAATAATGTCAAGCAGTTCAAAAAATACGTGGATAATCCAAAGCTGAGGGAGCTTCTGATAATTGGTGGCG
TGGCAGCCCGGGATCAGCTCTCTGTCCTGGAGCAGGGGGTGGACATTGTGGTTGGCACTCCAGGAAGGCTGGATGACTTG
GTGTCCACTGGGAAACTCAACTTATCTCAGATTCGATTCTTGGTTCTGGATGAAGCCGACGGCCTTCTTTCCCAGGGCTA
TTCTGACTTCATCAATAGGATTCACAGTCAAGATTCCTCAGATTACTTCTGATGGGAAAAAACTTCAGGTCATTGTCTGC
TCAGCCACTCTCCACTCTTTTGATGTCAAGAAGCTTTCTGAAAAGATCATGCATTTCCCTACCTGGGTTGATTTGAAAGG
AGAGGATTCAGTCCCTGAAACCGTGCACCATGTTGTTGTTCCTGTGAATCCCAAAACAGACAGGCTGTGGGAGAGGCTGG
GCAAGAACCACATCCGAACTGACGAAGTCCACGCAAAAGACAACACCAGACCTGGTGCCAACAGCCCTGAGATGTGGTCT
GAAGCCATAAAGATCCTGAAGGGGGAGTACACTGTCCGGGCCATCAAGGAACACAAGATGGACCAAGCAATAATCTTCTG
TAGAACCAAGATTGACTGTGACAACTTGGAGCAGTATTTCATGCAGCAAGGAGGAGGTCCAGACAAGAAAGGACATCAGT
TCTCCTGTGTGTGTCTTCACGGTGACAGAAAGCCTCATGAGAGGAAGAAAAACTTGGAGAGATTTAAGAAAGGT

Alignment

ORF - retro_meug_555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 76.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGVMPEIAQAVEEMDWLLPTDI-QAESIPLILGGGDVLMXXXXXXXXXXAFSIPVIQIVYETLKDQQEGK
          MGVMPE.AQA.EEMDW.LPTDI.QAESI.LILGGGDVLM..........AFSIPVIQIVYETLKDQQEGK
Retrocopy MGVMPENAQAMEEMDWFLPTDI<QAESILLILGGGDVLMAAETGSGKTGAFSIPVIQIVYETLKDQQEGK

Parental  KGKTTVKTGAAVLNKWQMNPYDRGSAFAIGSDGLCCQSREVKEWHGCRSTKGVMKGKHYYEVSCHDQGLC
          KGKTTVKTGAAVLNKWQMNPYD.GSAFAIGSDGLCCQSREVKEWHGCRSTKGVMKGKH.YEVSCHDQGLC
Retrocopy KGKTTVKTGAAVLNKWQMNPYDKGSAFAIGSDGLCCQSREVKEWHGCRSTKGVMKGKHNYEVSCHDQGLC

Parental  RVGWSTSQASLDLGTDKFGFGFGGTGKKSHNKQFDNYGEEFTMHDTIGCYLDVDKGQVKFSKNGKDLGLA
          RVGWSTSQASLDLGTDKFGFGFGGTGKKSHNKQFDNYGEEFTMHDTIGCYLDVDKGQVKFSKNGKDLGLA
Retrocopy RVGWSTSQASLDLGTDKFGFGFGGTGKKSHNKQFDNYGEEFTMHDTIGCYLDVDKGQVKFSKNGKDLGLA

Parental  FEIPAHLKNQAFFAACVLKNAELKFNFGEEEFKFPPKDGFVGLCKASDGHVVKSQHTGSAQVAQTKFLPN
          F.IPAHLKNQAFFAACVLKNAELKFNFGEEEFKFPPKDGFVGLCKASDGHVVKSQHTGSAQVAQTKFLPN
Retrocopy FKIPAHLKNQAFFAACVLKNAELKFNFGEEEFKFPPKDGFVGLCKASDGHVVKSQHTGSAQVAQTKFLPN

Parental  APKALIVEPSRELAEQTLNNVKQFKKYVDNPKLRELLIIGGVAARDQLSVLEQGVDIVVGTPGRLDDLVS
          APKALIVEPSRELAEQTLNNVKQFKKYVDNPKLRELLIIGGVAARDQLSVLEQGVDIVVGTPGRLDDLVS
Retrocopy APKALIVEPSRELAEQTLNNVKQFKKYVDNPKLRELLIIGGVAARDQLSVLEQGVDIVVGTPGRLDDLVS

Parental  TGKLNLSQIRFLVLDEADGLLSQGYSDFINRIHSQ-IPQITSDGKRLQVIVCSATLHSFDVKKLSEKIMH
          TGKLNLSQIRFLVLDEADGLLSQGYSDFINRIHSQ.IPQITSDGK.LQVIVCSATLHSFDVKKLSEKIMH
Retrocopy TGKLNLSQIRFLVLDEADGLLSQGYSDFINRIHSQ>IPQITSDGKKLQVIVCSATLHSFDVKKLSEKIMH

Parental  FPTWVDLKGEDSVPETVHHVVVHGNPKTDRLWEXXXXXXXXTDEVHAKDNTRPGANSPEMWSEAIKILKG
          FPTWVDLKGEDSVPETVHHVVV..NPKTDRLWE........TDEVHAKDNTRPGANSPEMWSEAIKILKG
Retrocopy FPTWVDLKGEDSVPETVHHVVVPVNPKTDRLWERLGKNHIRTDEVHAKDNTRPGANSPEMWSEAIKILKG

Parental  EYTVRAIKEHKMDQAIIFCRTKIDCDNLEQYFMQQGGGPDKKGHQFSCVCLHGDRKPHERKQNLERFKKG
          EYTVRAIKEHKMDQAIIFCRTKIDCDNLEQYFMQQGGGPDKKGHQFSCVCLHGDRKPHERK.NLERFKKG
Retrocopy EYTVRAIKEHKMDQAIIFCRTKIDCDNLEQYFMQQGGGPDKKGHQFSCVCLHGDRKPHERKKNLERFKKG

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_555 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_555 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	ENSMEUG00000008254	1 retrocopy	retro_meug_555 ,
Myotis lucifugus	ENSMLUG00000003027	1 retrocopy	retro_mluc_1223,
Otolemur garnettii	ENSOGAG00000008730	1 retrocopy	retro_ogar_2862,