RetrogeneDB ID: retro_mmus_2865

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:108563607..108565588(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000043024
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ddx18
• Ensembl ID: ENSMUSG00000001674
• Aliases: Ddx18, 2310005B10Rik
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:MGI Symbol;Acc:MGI:1914192]

Sequence

>retro_mmus_2865
ATGTCGCAGTTACAGATGAAACTCCTGCGCAGGAAGATCGAGAAGCGGAATGCCAAGCTGCGGCAGCGAAACCTGAAGCT
GCAAGAAGCATCAGACACAAGCCTGTCCCAACCTCAAAATGGAGATGTGCCTAAAGAAACAGGAAAAGGTGGAAAAGCGA
AAAAGGCCCTGAAACGTTCTGTGCCTGTGGACTCAGCAGAAGCACAAAGTGGAGGCATGCCTGAGGAGACCTTGGAAAAT
GGCAAAGTTAAAAAGTCACCCCAGAAACTCACAACTTTAGCCAACGGAGAAGCAGCACCAACACCACCTCCTGATTCAGA
AGTAAAAAAGAAAAAGAAGAAAAAGAGGAAAATGGCAAATGATGCCGGGCCTGATACAAAAAAAGCGAAAACTGAAGAAA
GTGCTGAGGCTTGTGAGGAACCAGAAGATGATGTGAAAAAGGCAGATGACAGCGAGGTGCCCAGCCTGCCACTAGGACTG
ACAGGTGCTTTTGAGGACACTTCATTTGCTTCCTTGTCTAATCTCGTCAATGAGAACACCCTGAAGGCCATAGAAGAAAT
GGGCTTCAAGCACATGACGGAGATCCAGCATAAAAGTATCAGGCCACTTCTGGAAGGCAGGGACCTTCTGGCGGCTGCAA
AAACCGGCAGTGGCAAAACCCTCGCTTTCCTTATCCCTGTGATCGAGCTCATTGTCAAGTTGAAGTTCATGCCCAGGAAT
GGAACAGGAGTCCTGATTCTCTCTCCTACCAGAGAACTGGCCATGCAGACCTTTGGTGTTCTCAAGGAGCTGATGACGCA
CCACGTTCACACGTATGGGCTGATCATGGGCGGCAGCAACAGGTCTGCTGAAAGTGCAGAAGCTCCTCAATGGGATCAAC
ATCATCGTGGCCACGCCCGGCCGGCTCCTGGACCACATGCAGAACACGCCAGGGTTTATGTACAAGAACCTGCAGTGTCT
GGTTATTGATGAGGCTGACCGTATCTTGGATGTTGGGTTTGAAGAAGAATTAAAGCAAATTATTAAACTTTTGCCAGCAC
GTAGGCAAACCATGCTCTTTTCTGCCACACAAACTCGAAAAGTTGAAGACTTGGCAAGAATTTCTCTGAAAAAGGAGCCT
TTGTACGTGGGTGTTGATGACGACAAAGAGGTTGCCACAGTGGATGGCCTTGAGCAGGGCTATGTTGTTTGTCCCTCTGA
GAAGAGGTTCCTTCTGCTTTTCACATTCCTTAAGAAGAACCGGAAGAAGAAAGTGATGGTCTTCTTTTCATCTTGTATGT
CTGTGAAATACCACTATGAGCTGTTGAACTACATTGACCTTCCCGTCTTGGCCATCCATGGAAAGCAAAAGCAAAATAAG
CAAACAACCACGTTTTTCCAGTTCTGCAACTCGGATTCAGGAATACTGCTGTGTACTGATGTGGCAGCCAGAGGGCTGGA
CATCCCTGAAGTGGACTGGATTGTTCAGTACGACCCTCCCGATGACCCCAAGGAATACATTCATCGTGTTGGTAGAACAG
CCAGGGGCCTGAATGGAAGAGGGCACGCCCTGCTCATCCTGCGCCCTGAAGAGTTGGGTTTCCTTCGTTACTTGAAACAG
TTCAAGGTTCCATTGAATCAGTTTGACTTCTCCTGGTCTAAAGTTTCTGATATCCAGTCTCAGCCGGAAAAACTGATCGA
AAAGAACTACTTTCTCCACAAGTCTGCCCAGGAAGCATACAAATCCTACATACGAGCATATGACTCTCACTCTCTCAAGC
AGATCTTCAACGTGAACAACTTAAATCTGCCTCAGGTTGCTCTGTCTTTTGGTTTTAAGGTCCCTCCTTTTGTTGATCTG
AATGTGAGCAGCCATGATGGCAAGCTTAAGAAGAGAGGCGGTGGTGGCGGATTCGGCTACCAGAAAACAAAGAAAGTGGA
GAAGTCCAAGATCTTTAAACACATCAGTAAGAAGCCAGCAGACCGCAGGCAGTTCTCACAC

Alignment

ORF - retro_mmus_2865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQLQMKLLRRKIEKRNAKLRQRNLKLQETSDTSLSQPQNGDVPKETGKGGKVKKALKRSVPVDSAEAQS
          MSQLQMKLLRRKIEKRNAKLRQRNLKLQE.SDTSLSQPQNGDVPKETGKGGK.KKALKRSVPVDSAEAQS
Retrocopy MSQLQMKLLRRKIEKRNAKLRQRNLKLQEASDTSLSQPQNGDVPKETGKGGKAKKALKRSVPVDSAEAQS

Parental  GGMPEETLENGKVKKSPQKLTTLANGEAAPTPPPDSEVKKKKKKKRKMANDAGPDTKKAKTEESAEACEE
          GGMPEETLENGKVKKSPQKLTTLANGEAAPTPPPD.............ANDAGPDTKKAKTEESAEACEE
Retrocopy GGMPEETLENGKVKKSPQKLTTLANGEAAPTPPPDXXXXXXXXXXXXXANDAGPDTKKAKTEESAEACEE

Parental  PEDDVKKADDSEVPSLPLGLTGAFEDTSFASLSNLVNENTLKAIEEMGFKRMTEIQHKSIRPLLEGRDLL
          PEDDVKKADDSEVPSLPLGLTGAFEDTSFASLSNLVNENTLKAIEEMGFK.MTEIQHKSIRPLLEGRDLL
Retrocopy PEDDVKKADDSEVPSLPLGLTGAFEDTSFASLSNLVNENTLKAIEEMGFKHMTEIQHKSIRPLLEGRDLL

Parental  AAAKTGSGKTLAFLIPVIELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSN
          AAAKTGSGKTLAFLIPVIELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSN
Retrocopy AAAKTGSGKTLAFLIPVIELIVKLKFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSN

Parental  RSAE-VQKLLNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPARRQ
          RSAE.VQKLLNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPARRQ
Retrocopy RSAE>VQKLLNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPARRQ

Parental  TMLFSATQTRKVEDLARISLKKEPLYVGVDDDKEVATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKVM
          TMLFSATQTRKVEDLARISLKKEPLYVGVDDDKEVATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKVM
Retrocopy TMLFSATQTRKVEDLARISLKKEPLYVGVDDDKEVATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKVM

Parental  VFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGILLCTDVAARGLDIPEVDWIVQ
          VFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNK.TTTFFQFCN.DSGILLCTDVAARGLDIPEVDWIVQ
Retrocopy VFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKQTTTFFQFCNSDSGILLCTDVAARGLDIPEVDWIVQ

Parental  YDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLNQFDFSWSKVSDIQSQLEKLI
          YDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQ.KVPLNQFDFSWSKVSDIQSQ.EKLI
Retrocopy YDPPDDPKEYIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQFKVPLNQFDFSWSKVSDIQSQPEKLI

Parental  EKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLNVSSHDGKLKKRGGGG
          EKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLNVSSHDGKLKKRGGGG
Retrocopy EKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDLNVSSHDGKLKKRGGGG

Parental  GFGYQKTKKVEKSKIFKHISKKPADRRQFSH
          GFGYQKTKKVEKSKIFKHISKKPADRRQFSH
Retrocopy GFGYQKTKKVEKSKIFKHISKKPADRRQFSH

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	0.05 RPM	9.30 RPM
SRP007412_cerebellum	0.09 RPM	9.25 RPM
SRP007412_heart	0.06 RPM	8.16 RPM
SRP007412_kidney	0.15 RPM	9.45 RPM
SRP007412_liver	0.05 RPM	7.65 RPM
SRP007412_testis	0.05 RPM	20.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2865 was not detected

EST

No EST(s) were mapped for retro_mmus_2865 retrocopy.

TSS

No TSS is located nearby retro_mmus_2865 retrocopy 5' end.

Lab

retro_mmus_2865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2865 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004950	2 retrocopies	retro_cfam_1404, retro_cfam_2116,
Callithrix jacchus	ENSCJAG00000021414	5 retrocopies	retro_cjac_2309, retro_cjac_2743, retro_cjac_4179, retro_cjac_644, retro_cjac_753,
Gorilla gorilla	ENSGGOG00000028420	4 retrocopies	retro_ggor_1201, retro_ggor_2189, retro_ggor_2402, retro_ggor_535,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Mus musculus	ENSMUSG00000001674	1 retrocopy	retro_mmus_2865 ,