RetrogeneDB ID: retro_ecab_8

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:96257113..96258370(+)
• Located in intron of: ENSECAG00000007303

Retrocopy information

• Ensembl ID: ENSECAG00000004989
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000017638
• Aliases: None
• Description: None

Sequence

>retro_ecab_8
TTAAGAAGAAACTTCCTGACTTGCCTGTCTTCTTGGAAAGCTCCTCCTCGCATCCCCAGATCTTCCCAGTCAGAAGCTCT
ACTCAATATAGCAAATAATGGGCTCCCCTACGCCCCACTGCAAACATTCACAGAGGAGGAGACGATGCTAAAGAGGACAG
TTGAAAGATTTGCCCAGGAACAAATTGCTCCTTTGGTTTTAACAATGGATGAAAATTCAAAAGTGGAAAAATCAGTAATA
CAAGGATTATTTCAACATGGGTTGATGGGAATTGAAATTGACACCATCTATGGAGGAACGGGAGCTTCGTTTTTCTCCTC
TGTCCTAGCGATAGAGGAATTAGCCAAAGTTGATGCATCTGTGGCTTTGTTTTGTGACCTCCAGAACACACTAATTAACA
CACTGATCATGAAACATGGAACAGAAGAACAAAAGGCTACCTATTTGACCAAGCTAGCTACAGAAGAAATAGGAAGTTTC
TGCCTTTCAGAGGCTGGAGCAGGAAGCGATTCATTTAGTCTGAAGACCAGAGCTGATAAAAAGGGAGATTATTTTGTCAT
CAACGGGTCAAAGATGTGGATCAGCCATGCTGAGTACGCAGGGCTCTTCCTGGTGATGGCAAACGTCGACCCTACCAGGG
GGTATAAAGGAATCACCTGCTTCTTAGTAGATCGTGGTACTGAAGGGCTTCATATAGGGAAACCAGAAAACAAATTGGGA
CTCAGAGCTTCTTGCACCTGTCCATTAACATTTGACAATGTCAAGGTTCCAGAAGCCAATGTCCTGGGACAAATTGGACA
TGGTTACAAGTATGCCATAGGGATGCTTAATAAAGGTAGAGTAGGAATTGCTGCACAGATGCTGGGACTGGCTCAAGGAT
GTTTTGACTACACTATTCCATATATTAAAGAAAGGGTACAATTTGGCACCAGATTATTTGACTTCCAGGGGCTCCAACAC
CAAGTGGCTCACGTGGCCACTCAGCTGGAAGCTGCAAGATTACTAACATACAACACAGCCAGGCTTGCGGAAGCTGGAAG
GCCGTTCATAAAAGAAGCATCTATGGCCAAATACTATGCATCAGAGATCGCGGGACGAACAACTAGTAAATGTATCGACT
GGATGGGAGGAGCGGGCTACGTCAAAGCTTACCCTGTGGAAAAGTACTTCCGAAATGCCAAGATTGGTACAATATATGAA
GGAACTTCAAATATTCAGCTGAACACCATTGCCAAGCACATCGATGCAGAATACTGA

Alignment

ORF - retro_ecab_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRRNFLTCLSSWKAPPRIPRSSQSEALLNIANNGLPYAPLQTFTEEEMMLKRTVERFAQEQIAPLVLTMD
          LRRNFLTCLSSWKAPPRIPRSSQSEALLNIANNGLPYAPLQTFTEEE.MLKRTVERFAQEQIAPLVLTMD
Retrocopy LRRNFLTCLSSWKAPPRIPRSSQSEALLNIANNGLPYAPLQTFTEEETMLKRTVERFAQEQIAPLVLTMD

Parental  ENSKVEKSVIQGLFQHGLMGIEIDTIYGGTGASFFSSVLAIEELAKVDASVALFCDLQNTLINTLIMKHG
          ENSKVEKSVIQGLFQHGLMGIEIDTIYGGTGASFFSSVLAIEELAKVDASVALFCDLQNTLINTLIMKHG
Retrocopy ENSKVEKSVIQGLFQHGLMGIEIDTIYGGTGASFFSSVLAIEELAKVDASVALFCDLQNTLINTLIMKHG

Parental  TEEQKATYLTKLATEEIGSFCLSEAGAGSDSFSLKTRADKKGDYFVINGSKMWISHAEYAGLFLVMANVD
          TEEQKATYLTKLATEEIGSFCLSEAGAGSDSFSLKTRADKKGDYFVINGSKMWISHAEYAGLFLVMANVD
Retrocopy TEEQKATYLTKLATEEIGSFCLSEAGAGSDSFSLKTRADKKGDYFVINGSKMWISHAEYAGLFLVMANVD

Parental  PTRGYKGITCFLVDRGTEGLHIGKPENKLGLRASCTCPLTFDNVKVPEANVLGQIGHGYKYAIGMLNKGR
          PTRGYKGITCFLVDRGTEGLHIGKPENKLGLRASCTCPLTFDNVKVPEANVLGQIGHGYKYAIGMLNKGR
Retrocopy PTRGYKGITCFLVDRGTEGLHIGKPENKLGLRASCTCPLTFDNVKVPEANVLGQIGHGYKYAIGMLNKGR

Parental  VGIAAQMLGLAQGCFDYTIPYIKERVQFGTRLFDFQGLQHQVAHVATQLEAARLLTYNAARLAEAGRPFI
          VGIAAQMLGLAQGCFDYTIPYIKERVQFGTRLFDFQGLQHQVAHVATQLEAARLLTYN.ARLAEAGRPFI
Retrocopy VGIAAQMLGLAQGCFDYTIPYIKERVQFGTRLFDFQGLQHQVAHVATQLEAARLLTYNTARLAEAGRPFI

Parental  KEASMAKYYASEIAGRTTSKCIDWMGGAGYVKAYPVEKYFRDAKIGTIYEGTSNIQLNTIAKHIDAEY
          KEASMAKYYASEIAGRTTSKCIDWMGGAGYVKAYPVEKYFR.AKIGTIYEGTSNIQLNTIAKHIDAEY
Retrocopy KEASMAKYYASEIAGRTTSKCIDWMGGAGYVKAYPVEKYFRNAKIGTIYEGTSNIQLNTIAKHIDAEY

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	1.89 RPM
SRP021940_cerebellum	0.10 RPM	5.30 RPM
SRP021940_embryo	0.05 RPM	4.58 RPM
SRP021940_placental_villous	0.05 RPM	1.30 RPM
SRP021940_synovial_membrane	0.03 RPM	2.09 RPM
SRP021940_testis	0.00 RPM	7.99 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_8 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_8 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017638	1 retrocopy	retro_ecab_8 ,
Rattus norvegicus	ENSRNOG00000020624	4 retrocopies	retro_rnor_2753, retro_rnor_2762, retro_rnor_2763, retro_rnor_2764,