RetrogeneDB ID: retro_ecab_527

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:109580431..109581719(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000022993
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTMR1
• Ensembl ID: ENSECAG00000007323
• Aliases: None
• Description: myotubularin related protein 1 [Source:HGNC Symbol;Acc:7449]

Sequence

>retro_ecab_527
GAATGGTGTAAACAGCTTATAGCTTCTAGCATTTCTAGTCAGATTTCAGGTCCAGTGACATCAGAAAATGTATCCAGAGA
TTACAAGGCTCTAAGAGATGGAAATAAGCTGGCACAGATGGAAGAAGCACCACTTTTTCCAGGAGAGTCGATCAAGGCCG
TTGTGAAAGACGTCACGTATGTCTGCCCATTTATGGAAGCAGTGAGTGGAACCCTGACAGTGACTGACTTCAAGAGGTAC
TTCAGAAATGTAGAGGGACCCACATTTCGTCCTTGATGTTCCCCTGGGTGTGATCAGCAGAGTTGAGAAGATTGGCGCGC
AGAGCCACGAGGACAATTCTTGTGGTATAGAGATCGTGTGCAAGGATATGAGGAACTTACGACTTGCTTACAAACAGGAA
GAACAGAGTAAACTGGGGATATTTGAAAACCTCACCGAACGTGCATTTCCTCTTTCCAACGGACAGGCACTCTTTGCATT
CAACCATAAAGAGAAATTTCCAATTAATGCATGGAAAGTTTATGATCCAGTATCTGAATATAAGAGACAGGGCTTGCCAA
ATGAGAGTTGGAAAATATCCAAAGTAAACAGTAATTATGAGCTCTGTGACACCTACCCTGCCATCATTGTTGTGCCAACT
AGTGTGAAAGATGATGACCTTTCAAAAGTGGCAGCCTTTCGAGCAAAAGGCAGAGTCCCTGTGTTGTCATGGATTCATCC
AGAAAGTGAGGCAACGATTACCCGTTGCAGCCAGCTACTTGTGGGTCCCAATGATAAATGCTGCAAAGAAGATGAAAAAT
ACTTGCAAACAATAATGGATGCTTATGCACAGTCTCACAAACTTATCATCTTTGATGCCCGACAAAACAGTGTTGCTGAT
ACTAACAAGGCAAAGGGTGGAGGATATGAAACTGAAAGTGCTTACCCCAACGCAGAACTCGTGTTCTTGGAGATCCACAA
CATTCACGTGTTGAGAGAGTCACTACGTAAATTGAAAGAGATTGTGCACCCTTCCATCGATGAGACACAGTGGCTGTCCA
ACGTGGATGGGACGCATTGGCTAGAGTATATAAGGATGCTTCTTGCTGGGGCAGTAAGAATTGCCGATAAAATAGAATCT
GGGAAAACTTCGGTGGTGGTGCATTGCAGCGATGGTTGGGACCGAACAGCCCAGCTGATGTCTCCGGCCATGCTGATGTT
GGACAGTTATTATCGTACCATTAAAGGGTTCGAGGCTCTCATAGAAAAGGAGTGGATCAGCTTTGGACATAAGTTTGCAC
TGTGTGTG

Alignment

ORF - retro_ecab_527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.04 %
• Parental protein coverage: 69.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EWCKQLIAATISSQISGSVTSENVSRDYKALRDGNKLAQMEEAPLFPGESIKAIVKDVMYICPFMGAVSG
          EWCKQLIA..ISSQISG.VTSENVSRDYKALRDGNKLAQMEEAPLFPGESIKA.VKDV.Y.CPFM.AVSG
Retrocopy EWCKQLIASSISSQISGPVTSENVSRDYKALRDGNKLAQMEEAPLFPGESIKAVVKDVTYVCPFMEAVSG

Parental  TLTVTDFKMYFKNVERDPHF-VLDVPLGVISRVEKIGAQSHGDNSCGIEIVCKDMRNLRLAYKQEEQSKL
          TLTVTDFK.YF.NVE..P.F.VLDVPLGVISRVEKIGAQSH.DNSCGIEIVCKDMRNLRLAYKQEEQSKL
Retrocopy TLTVTDFKRYFRNVE-GPTF>VLDVPLGVISRVEKIGAQSHEDNSCGIEIVCKDMRNLRLAYKQEEQSKL

Parental  GIFENLTKHAFPLSNGQALFAFNYKEKFPINGWKVYDPVSEYKRQGLPNESWKISKVNSNYELCDTYPAI
          GIFENLT..AFPLSNGQALFAFN.KEKFPIN.WKVYDPVSEYKRQGLPNESWKISKVNSNYELCDTYPAI
Retrocopy GIFENLTERAFPLSNGQALFAFNHKEKFPINAWKVYDPVSEYKRQGLPNESWKISKVNSNYELCDTYPAI

Parental  IVVPTSVKDDDLSKVAAFRAKGRVPVLSWIHPESQATITRCSQPLVGPNDKRCKEDEKYLQTIMDANAQS
          IVVPTSVKDDDLSKVAAFRAKGRVPVLSWIHPES.ATITRCSQ.LVGPNDK.CKEDEKYLQTIMDA.AQS
Retrocopy IVVPTSVKDDDLSKVAAFRAKGRVPVLSWIHPESEATITRCSQLLVGPNDKCCKEDEKYLQTIMDAYAQS

Parental  HKLIIFDARQNSVADTNKAKGGGYESESAYPNAELVFLEIHNIHVMRESLRKLKEIVYPSIDEARWLSNV
          HKLIIFDARQNSVADTNKAKGGGYE.ESAYPNAELVFLEIHNIHV.RESLRKLKEIV.PSIDE..WLSNV
Retrocopy HKLIIFDARQNSVADTNKAKGGGYETESAYPNAELVFLEIHNIHVLRESLRKLKEIVHPSIDETQWLSNV

Parental  DGTHWLEYIRMLLAGAVRIADKIESGKTSVVVHCSDGWDRTAQLTSLAMLMLDSYYRTIKGFEALIEKEW
          DGTHWLEYIRMLLAGAVRIADKIESGKTSVVVHCSDGWDRTAQL.S.AMLMLDSYYRTIKGFEALIEKEW
Retrocopy DGTHWLEYIRMLLAGAVRIADKIESGKTSVVVHCSDGWDRTAQLMSPAMLMLDSYYRTIKGFEALIEKEW

Parental  ISFGHKFALRV
          ISFGHKFAL.V
Retrocopy ISFGHKFALCV

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
SRP021940_articular_cartilage	0.00 RPM	6.97 RPM
SRP021940_cerebellum	0.31 RPM	21.03 RPM
SRP021940_embryo	0.31 RPM	16.88 RPM
SRP021940_placental_villous	0.00 RPM	16.50 RPM
SRP021940_synovial_membrane	0.00 RPM	10.57 RPM
SRP021940_testis	0.06 RPM	3.77 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_527 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_527 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013433	1 retrocopy	retro_dnov_2271,
Equus caballus	ENSECAG00000007323	1 retrocopy	retro_ecab_527 ,
Macropus eugenii	ENSMEUG00000012257	1 retrocopy	retro_meug_1367,