RetrogeneDB ID: retro_ecab_1029

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:58740964..58741421(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D1
• Ensembl ID: ENSECAG00000019479
• Aliases: None
• Description: SFT2 domain containing 1 [Source:HGNC Symbol;Acc:21102]

Sequence

>retro_ecab_1029
ATGGAGAGGCCGTGGAAGGTCCTGAGCAGCCAGGATGACAAGGAGCAGAACCTAACTGCAAAGGGCCTGGATGACTTGTC
CCTTAGTTTCAACACTAGATTGAATTGATTTGTCATATGCTTTGTATGTGGCATTTCTGTTCTATCCTTGGAACTGGATT
GCTGTGGTTTCTGGTGGCATAAAACTTTTTACACTCTTTTATATCCGGGGAAATATTGCTGTATGAGCTTTTTAATGGGC
CCCATGAGGCAACGGAAGGAAATGTTTGAAACAAGATTATCTTGCAATAATTATTATCCTTTTTTGCTTCATATTTACCA
TTTGTGCTTCTCTTTGGGGACATAAGAAGGGACTGGCCTTATTGTTGAGCATATTGCAGTTCTTGTGAATGACCTGGTAT
AGTCTATGGTGGGTCCCATATCCTAGAGATGCAGTAATTAAATGCTATTCTGTCCTA

Alignment

ORF - retro_ecab_1029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.6 %
• Parental protein coverage: 98.74 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEKLRRVLSGQDDEEQGLTSQVLDASTLSFNTRLKWFAICFVSGV-FFSLLGTGLLW-LPGGIKLFAVFY
          ME....VLS.QDD.EQ.LT...LD...LSFNTRL..F.ICFV.G..F.S.LGTGLLW...GGIKLF..FY
Retrocopy MERPWKVLSSQDDKEQNLTAKGLDDLSLSFNTRLN*FVICFVCGI<FCSILGTGLLW<VSGGIKLFTLFY

Parental  TLGNIAALASTCFLMGPVKQLKKMFETTRLFATVIMLLCFVFTLCAALWWHKRALALLFCILQFLSMTWY
          ..GNIA..A...F...P.....K......L....I...CF.FT.CA.LW.HK..LALL..ILQFL.MTWY
Retrocopy IRGNIAV*A---F*WAP*GNGRKCLKQDYLAIIIIL-FCFIFTICASLWGHKKGLALLLSILQFL*MTWY

Parental  SLSYIPYARDAVIKCCSSL
          SL...PY.RDAVIKC.S.L
Retrocopy SLWWVPYPRDAVIKCYSVL

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	3.54 RPM
SRP021940_cerebellum	0.00 RPM	14.23 RPM
SRP021940_embryo	0.00 RPM	5.22 RPM
SRP021940_placental_villous	0.00 RPM	24.68 RPM
SRP021940_synovial_membrane	0.00 RPM	9.66 RPM
SRP021940_testis	0.00 RPM	20.21 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1029 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1029 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1029 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_546
Sus scrofa	retro_sscr_751

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458, retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029 ,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37, retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181,
Pteropus vampyrus	ENSPVAG00000012673	3 retrocopies	retro_pvam_1340, retro_pvam_465, retro_pvam_559,
Sus scrofa	ENSSSCG00000004020	1 retrocopy	retro_sscr_751,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,
Tursiops truncatus	ENSTTRG00000004447	2 retrocopies	retro_ttru_1353, retro_ttru_624,