RetrogeneDB ID: retro_ecab_1097

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:6128044..6128473(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSECAG00000000497
• Aliases: None
• Description: THO complex 7 homolog (Drosophila) [Source:HGNC Symbol;Acc:29874]

Sequence

>retro_ecab_1097
AGAAAGCACCTCTTAATTGGTGGGGACGGTCAGAGAATTAATCAGCTAGTGAAGAATTTCATTAAATGGTGCAACTCTGG
ATCCCAGGAGGAGGGATATGGCTGGTGCCAATGTACGCTGAGCACAATGTCACAATGCGGCTTTTCAATCGGCAAAACCT
CACTGGTACATGATCCAAATCCCAGAGAACTGAAGAATTATGAAAAAGTGTGCTAAGATATAGAATGTAGCATAGCTGCA
GAACATGAAAGGAAAATGCTGAAGGCAAAATGCAGATTCTCTCAAGCAAAATGAGCATGGAAAAAATAGTCAGGAACCCA
ATGCTTTTCTGAAAGTATTCCAGCATCATCCAAACAGGCATGAAGCAGAAAAGAACAACAGGCTCTGGGAAAAGACTTAG
AGCCTTTTTCAAACATACTAAAGAAAATA

Alignment

ORF - retro_ecab_1097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.39 %
• Parental protein coverage: 73.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKRLLIDGDGAGDDRRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSMGKTLLVYDMNLREMEN
          RK.LLI.GDG.....RIN.LVK.FIKWCNSGSQEEGY...Q..LST.SQC.FS.GKT.LV.D.N.RE..N
Retrocopy RKHLLIGGDG----QRINQLVKNFIKWCNSGSQEEGYGWCQCTLSTMSQCGFSIGKTSLVHDPNPRELKN

Parental  YEKIYKEIECSIAGAHE-KIAECKKQILQAK-RIRKNRQEYDALAKVIQHHPDRHE-TLKELEALGKELE
          YEK....IECSIA..HE.K....K....QAK....KN.QE..A..KV.QHHP.RHE...KE..ALGK.LE
Retrocopy YEKVC*DIECSIAAEHERKMLKAKCRFSQAK>EHGKNSQEPNAFLKVFQHHPNRHE<SRKEQQALGKDLE

Parental  HLSHIKESV
          ..S.I....
Retrocopy PFSNILKKI

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	6.14 RPM
SRP021940_cerebellum	0.00 RPM	6.65 RPM
SRP021940_embryo	0.00 RPM	7.88 RPM
SRP021940_placental_villous	0.00 RPM	13.09 RPM
SRP021940_synovial_membrane	0.00 RPM	5.66 RPM
SRP021940_testis	0.64 RPM	7.16 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1097 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1097 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1097 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Equus caballus	ENSECAG00000000497	1 retrocopy	retro_ecab_1097 ,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Ochotona princeps	ENSOPRG00000016403	2 retrocopies	retro_opri_1031, retro_opri_345,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Ictidomys tridecemlineatus	ENSSTOG00000012552	1 retrocopy	retro_itri_1425,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,