RetrogeneDB ID: retro_ecab_601

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:2722466..2723123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA3
• Ensembl ID: ENSECAG00000018186
• Aliases: None
• Description: transcriptional adaptor 3 [Source:HGNC Symbol;Acc:19422]

Sequence

>retro_ecab_601
AGCAGAAGGATGGGCTGGGCTGACAAGAAGAAAGGCTTCATGGGGCCACTGACACAACTGGACACTAAAGATGTAGATAC
CCTGCTAAAGAAGTCTGAGGCCCAGCAGCCGGAAGATGGGTACCCCTTTGGTGCCCTGACGCAGAGCCTCCTGCAGGCCC
TGGTGGAGGAAAATATTATTTCCCCCGTGGAGGACTCTCCTATTCCTGACATGTCCGGGAAAGAACTGTGGGCTGATGGC
GTGAGCCCCTCCCCCGCAGTCAGACCAAGCCCTTCAGTGTGCCACACACCAAGTGCCTGGAGAGCCAGCCGCATCAAGGA
GGAGCTGATTGCCCAGGGCCTGCTGGAGTCTGAGGAACGCCCTGCAGAAGGCTCAGAGGATGAGGTCCTCGTGGAGCTGT
GCAGACAGCAGGCCGAGCTGAAGGCACTCAGTGCCCACAACCACACCAAGAAGCACGACCTGCTGAGGCTGGCAAAGGAG
GAGGTGAGCTGGCAAGATCTGAGGCAGCGGGTGCGCACGGCACACAACGAGGTCATGGTCACCTTCCGCAAGATCATTGC
TGCCCAGCAGAACAAGCGGACCCCCACCAAGAAAGAGAAGGACCAGGCCTGGAAGACTCTAAAGGAGTATGAGAGCATCC
TAAAGCTGCTGGACGGG

Alignment

ORF - retro_ecab_601 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.73 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARAAAVADKKKGLMGPLTELDTKDVDALLKKSEAQHEQPEDGCPFGALTQRLLQALVEENIISPMEDSPI
          .R....ADKKKG.MGPLT.LDTKDVD.LLKKSEAQ..QPEDG.PFGALTQ.LLQALVEENIISP.EDSPI
Retrocopy SRRMGWADKKKGFMGPLTQLDTKDVDTLLKKSEAQ--QPEDGYPFGALTQSLLQALVEENIISPVEDSPI

Parental  PDMSGKESGADGASTSPRNQNKPFSVPHTKSL--ESRIKEELIAQGLLESEERPAEDSEDEVLAELRKRQ
          PDMSGKE..ADG.S.SP.....P.SV.HT.S....SRIKEELIAQGLLESEERPAE.SEDEVL.EL...Q
Retrocopy PDMSGKELWADGVSPSPAVRPSP-SVCHTPSAWRASRIKEELIAQGLLESEERPAEGSEDEVLVELCRQQ

Parental  AELKALSAHNRTKKHDLLRLAKEEVSRQELRQRVRMADNEVMDAFRKIMAARQKKRTPTKKEKDQAWKTL
          AELKALSAHN.TKKHDLLRLAKEEVS.Q.LRQRVR.A.NEVM..FRKI.AA.Q.KRTPTKKEKDQAWKTL
Retrocopy AELKALSAHNHTKKHDLLRLAKEEVSWQDLRQRVRTAHNEVMVTFRKIIAAQQNKRTPTKKEKDQAWKTL

Parental  KERESILKLLDG
          KE.ESILKLLDG
Retrocopy KEYESILKLLDG

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	22.55 RPM
SRP021940_cerebellum	0.00 RPM	58.89 RPM
SRP021940_embryo	0.05 RPM	69.00 RPM
SRP021940_placental_villous	0.05 RPM	28.82 RPM
SRP021940_synovial_membrane	0.00 RPM	44.86 RPM
SRP021940_testis	0.06 RPM	258.14 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_601 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_601 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005324	2 retrocopies	retro_cfam_2011, retro_cfam_2106,
Equus caballus	ENSECAG00000018186	1 retrocopy	retro_ecab_601 ,
Mus musculus	ENSMUSG00000048930	2 retrocopies	retro_mmus_1999, retro_mmus_3497,
Otolemur garnettii	ENSOGAG00000034225	1 retrocopy	retro_ogar_362,
Rattus norvegicus	ENSRNOG00000008597	2 retrocopies	retro_rnor_1273, retro_rnor_1479,