RetrogeneDB ID: retro_cfam_1925

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:324026..325728(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000010702
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX21
• Ensembl ID: ENSCAFG00000013791
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 21 [Source:HGNC Symbol;Acc:2744]

Sequence

>retro_cfam_1925
CATTCTGGACTTGTCTCTAACACCAGTGAAACCCTAGGGGAAGAAAGTAACAGTGAGTTAGAGCAGGAAATGCCTGTGGA
ACAGAAAGAAGGAGCTTTCTCTAATTTTCCCATATCTGAAGAGACTATTAAACTTCTCAAAGCCCGTGGGGTGACCTTCC
TGTTTCCTATACAAGCAAAGACATTTTACCATGTCTATAGTGGAAAGGACTTAACTGCACAGGCGCGGACAGGAACTGGG
AAGACATTCTCCTTTGCCATCCCTTTGATTGCGAAGCTCCAGGGAGAACTGCAAGGCAGGAAAAGAGGTCGTGCCCCTCA
GGTACTGGTTCTTACACCCATGAAGGAGTTGGCAAATCAAGTAAGCAGAGACTTCAGTGACATCACAAGAAAGCTGGCGG
TGGCTTGTTTTTATGGTGGAACTCCCTATGGAGGTCAAATTGAAAGCATGTGGATTGGGATTGATATCCTGGTTGGGACC
CCAGGTCGTATCAAAGACCACCCTCAGAATGGCAAGCTAGATCTCACCAAACTTAAGCATGTTGTCCTGGATGAAGTTGA
CCAGATGTTAGATATGGGGTTTGCTGATCAAGTGGAAGAGATTTTAAGTGTGGCATACAAAAAAGATTCAGAAGACAATC
CCCAAACATTGCTTTTTTCTGCAACTTGCCCTCATTGGGTATATGATGTTGCTAAGAAATACATGAAATCTACATATGAA
CAGGTGGACCTGATTGGTAAAAAGACCCAGAAAATGGCAATAACCGTGGAGCACCTGGCTATCAAGTGCCACTGGACTCA
AAGGGCAGCAGTTATTGGGGATGCGATCCGAGTATACTCGTGGTTTTCACGGGCATACCATCATCTTCTACGAAACCAAG
AAAGAAGCCCAGGAGTTGTCACAGAATATGTCCATAAGGCAGGATGCCCAGTCATTGCATGGAGATATTCCTCAGAAGCA
GAGAGAAATCACTCTGAAAGGTTTTAGAAATGGTGATTTGGGAGTTTTGGTTGCAACTAATGTTGCTGCTCGTGGGTTAG
ACATCCCTGAGGTTGACCAGGTGATACAGAGTTCTCCACCAAAGGATGTGGAGTCCTATATTCATCGCTCTGGGAGGAGG
GGCAGAGCTGGAAGGACAGGGATTTGCATCTGCTTTTATCAGCACAAGGAGGAGTATCAGTTAGCACAAATGGAGCAAAA
AGCGGGAATTAAATTTAAACGAATAGGTGTTCCTTCTGCAACAAAGATCATAAAAGCTTCCAGCAAAGATGCCATCAGGC
TTTTGGATTCTGTGCCTCCCGCTGCCATTAGTCATTTCAAGCAGTCAGCGGAGAAACTAATAGAGGAGAAAGGAGCCGTG
GAAGCCCTGGCAGCAGCCTTGGCCCATATTTCAGGTGCCACATCAGTAGACCAGCGCTCTCTGATCAACTCAGATGCGGG
CTTTGTGACCATGATCTTACGATGCTCAATGGAAATGCCAAACATTAGTTATGCTTGGAAAGAACTTAAAGAGCAGCTGG
GAGAGGATATTGATTCCAAAGTGAAAGGAATGGTGTTTCTCAAAGGAAAGCAGGGAGTTTGCTTCGATGTCCCTACTGCA
GCAGTAACAGAAATACAGGAAAAATGGCATGATATGCGTCGCTGGCAGCTCTCTGTGGCCACGGAGCAACCAGAGCTGGA
AGGACCTCGGGAAAGATATCGA

Alignment

ORF - retro_cfam_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.73 %
• Parental protein coverage: 72.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSGLVSNTSETLGEESSSELEQEIPVEQKEGAFSNFPISEETIKLLKARGVTFLFPIQAKTFYHVYSGKD
          HSGLVSNTSETLGEES.SELEQE.PVEQKEGAFSNFPISEETIKLLKARGVTFLFPIQAKTFYHVYSGKD
Retrocopy HSGLVSNTSETLGEESNSELEQEMPVEQKEGAFSNFPISEETIKLLKARGVTFLFPIQAKTFYHVYSGKD

Parental  LIAQARTGTGKTFSFAIPLIVKLQGELQDRKRGRAPQVLVLAPTRELANQVSRDFSDITRKLAVACFYGG
          L.AQARTGTGKTFSFAIPLI.KLQGELQ.RKRGRAPQVLVL.P..ELANQVSRDFSDITRKLAVACFYGG
Retrocopy LTAQARTGTGKTFSFAIPLIAKLQGELQGRKRGRAPQVLVLTPMKELANQVSRDFSDITRKLAVACFYGG

Parental  TPYGGQIERMRNGIDILVGTPGRIKDHLQNGKLDLTKLKHVVLDEVDQMLDMGFADQVEEILSVAYKKDS
          TPYGGQIE.M..GIDILVGTPGRIKDH.QNGKLDLTKLKHVVLDEVDQMLDMGFADQVEEILSVAYKKDS
Retrocopy TPYGGQIESMWIGIDILVGTPGRIKDHPQNGKLDLTKLKHVVLDEVDQMLDMGFADQVEEILSVAYKKDS

Parental  EDNPQTLLFSATCPHWVYNVAKKYMKSTYEQVDLIGKKTQKTAITVEHLAIKCHWTQRAAVIGDVIRVYS
          EDNPQTLLFSATCPHWVY.VAKKYMKSTYEQVDLIGKKTQK.AITVEHLAIKCHWTQRAAVIGD.IRVYS
Retrocopy EDNPQTLLFSATCPHWVYDVAKKYMKSTYEQVDLIGKKTQKMAITVEHLAIKCHWTQRAAVIGDAIRVYS

Parental  -GFHGRTIIFCETKKEAQELSQNVSIRQDAQSLHGDIPQKQREITLKGFRNGDFGVLVATNVAARGLDIP
          .GFHG.TIIF.ETKKEAQELSQN.SIRQDAQSLHGDIPQKQREITLKGFRNGD.GVLVATNVAARGLDIP
Retrocopy >GFHGHTIIFYETKKEAQELSQNMSIRQDAQSLHGDIPQKQREITLKGFRNGDLGVLVATNVAARGLDIP

Parental  EVDLVIQSSPPKDVESYIHRSGRTGRAGRTGICICFYQHKEEYQLAQVEQKAGIKFKRIGVPSATEIIKA
          EVD.VIQSSPPKDVESYIHRSGR.GRAGRTGICICFYQHKEEYQLAQ.EQKAGIKFKRIGVPSAT.IIKA
Retrocopy EVDQVIQSSPPKDVESYIHRSGRRGRAGRTGICICFYQHKEEYQLAQMEQKAGIKFKRIGVPSATKIIKA

Parental  SSKDAIRLLDSVPPTAISHFKQSAEKLIEEKGAVEALAAALAHISGATSVDQRSLINSDAGFVTMILRCS
          SSKDAIRLLDSVPP.AISHFKQSAEKLIEEKGAVEALAAALAHISGATSVDQRSLINSDAGFVTMILRCS
Retrocopy SSKDAIRLLDSVPPAAISHFKQSAEKLIEEKGAVEALAAALAHISGATSVDQRSLINSDAGFVTMILRCS

Parental  IEMPNISYAWKELKEQLGEDIDSKVKGMVFLKGKQGVCFDVPTAALTEIQQEKWHDSRRWQLSVATEQPE
          .EMPNISYAWKELKEQLGEDIDSKVKGMVFLKGKQGVCFDVPTAA.TEI.QEKWHD.RRWQLSVATEQPE
Retrocopy MEMPNISYAWKELKEQLGEDIDSKVKGMVFLKGKQGVCFDVPTAAVTEI-QEKWHDMRRWQLSVATEQPE

Parental  LEGPREGYR
          LEGPRE.YR
Retrocopy LEGPRERYR

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
SRP012049_cerebellum	0.00 RPM	20.29 RPM
SRP017611_brain	0.00 RPM	8.89 RPM
SRP017611_kidney	0.07 RPM	20.47 RPM
SRP017611_liver	0.07 RPM	19.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1925 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1925 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013791	2 retrocopies	retro_cfam_1024, retro_cfam_1925 ,
Callithrix jacchus	ENSCJAG00000012876	1 retrocopy	retro_cjac_1912,
Macropus eugenii	ENSMEUG00000010586	1 retrocopy	retro_meug_1383,
Microcebus murinus	ENSMICG00000015112	1 retrocopy	retro_mmur_95,
Mus musculus	ENSMUSG00000020075	2 retrocopies	retro_mmus_582, retro_mmus_662,
Procavia capensis	ENSPCAG00000016697	1 retrocopy	retro_pcap_346,
Pongo abelii	ENSPPYG00000002389	1 retrocopy	retro_pabe_3816,
Tupaia belangeri	ENSTBEG00000002310	2 retrocopies	retro_tbel_1590, retro_tbel_4454,