RetrogeneDB ID: retro_ecab_288

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:19674539..19675297(-)
• Located in intron of: ENSECAG00000014460

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CAB39
• Ensembl ID: ENSECAG00000015288
• Aliases: None
• Description: calcium binding protein 39 [Source:HGNC Symbol;Acc:20292]

Sequence

>retro_ecab_288
TTGAAGGAAATTCCGTATGGTACAAATGAAAAAGAACCACAGACAGAAGCGGCGGCCAACTCGCTCAAGAACTCTGTAAC
AGTGGGCTCCTTAGCACCCTGGTAGCTGACTTACAGCTCATTGACTTTGAGGGCAAAAAAAGATGTGGCTCAAATTTTCA
ACAATATTCTCAGAAGACAAATTGGTACAAGAACTCCCACTGTTGAATACATCTGCACCCAACAGAATATTTTGTTCGTG
TTATTGAAAGGGTATGAATCTCCAGAAATAGCTCTAAATTGTGGAATAATGTTGAGAGAATGCATCAGACACGAACCACT
TGCAAAAATCATTTTTGGTCAGAACAATTTTATGATTTCTTCAGATGTGTCGAAATGTCAATATTTGACGTAGCTTCAGA
TGCATTCGCCACATTCAAGGATTTACTTACAAGACATAAATTGCTCAGTGCAGAATTTTTGGAACAGCATTATGATAGAT
TCTTCAGTGAACATGAGAAGTTACTTCATTCAGAAAATTAGGTGACAAAAAGACAGTCACCCAAGCTTCTCGGTGAGTTA
CTATTAGACAGACACAACTTCACGATTATGACAAAATCCATCAGTAAACCTGAGAACCTCAAATTAATGATGAACCTTCT
GCGAGACAAAAGTTGTAACATCCAATTTGAGGCCTTTCACATTTTTAAGGTGTTTGTAGCCAATCCTAACAAGACACAGC
CCATCCTCAACATCCTCCTCTAGAACCAGACCAAACTC

Alignment

ORF - retro_ecab_288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.19 %
• Parental protein coverage: 74.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKEILYGTNEKEPQTEAVA-QLAQELYNSGLLSTLVADLQLIDFEGKK-DVAQIFNNILRRQIGTRTPTV
          .KEI.YGTNEKEPQTEA.A.QLAQEL.NSGLLSTLVADLQLIDFEGKK.DVAQIFNNILRRQIGTRTPTV
Retrocopy LKEIPYGTNEKEPQTEAAA<QLAQELCNSGLLSTLVADLQLIDFEGKK>DVAQIFNNILRRQIGTRTPTV

Parental  EYICTQQNILFMLLKGYESPEIALNCGIMLRECIRHEPLAKIIL-WSEQFYDFFRYVEMSTFDIASDAFA
          EYICTQQNILF.LLKGYESPEIALNCGIMLRECIRHEPLAKII..WSEQFYDFFR.VEMS.FD.ASDAFA
Retrocopy EYICTQQNILFVLLKGYESPEIALNCGIMLRECIRHEPLAKIIF<WSEQFYDFFRCVEMSIFDVASDAFA

Parental  TFKDLLTRHKLLSAEFLEQHYDRFFSEYEKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPENL
          TFKDLLTRHKLLSAEFLEQHYDRFFSE.EKLLHSEN.VTKRQS.KLLGELLLDRHNFTIMTK.ISKPENL
Retrocopy TFKDLLTRHKLLSAEFLEQHYDRFFSEHEKLLHSEN*VTKRQSPKLLGELLLDRHNFTIMTKSISKPENL

Parental  KLMMNLLRDKSRNIQFEAFHVFKVFVANPNKTQPILDILLKNQTKL
          KLMMNLLRDKS.NIQFEAFH.FKVFVANPNKTQPIL.ILL.NQTKL
Retrocopy KLMMNLLRDKSCNIQFEAFHIFKVFVANPNKTQPILNILL*NQTKL

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	13.40 RPM
SRP021940_cerebellum	0.00 RPM	18.44 RPM
SRP021940_embryo	0.00 RPM	14.19 RPM
SRP021940_placental_villous	0.10 RPM	25.93 RPM
SRP021940_synovial_membrane	0.08 RPM	11.31 RPM
SRP021940_testis	0.06 RPM	27.24 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_288 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_288 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
Callithrix jacchus	ENSCJAG00000013349	1 retrocopy	retro_cjac_4227,
Equus caballus	ENSECAG00000015288	1 retrocopy	retro_ecab_288 ,
Otolemur garnettii	ENSOGAG00000002000	1 retrocopy	retro_ogar_1455,