RetrogeneDB ID: retro_ecab_791

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:63362488..63362923(+)
• Located in intron of: ENSECAG00000022057

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000024361
• Aliases: None
• Description: Sulfurtransferase [Source:UniProtKB/TrEMBL;Acc:F6XRG6]

Sequence

>retro_ecab_791
GCTGCCCTCTGGTCTTTGGATGCTATGCTCAAGGATTTGAGGTCAATAAAGGGAAGCTGCCAGAATTTCAGCATTTCCTT
CCTAAAGAAGTCATTTATCAAGAACCTAAAAACCTACTAAATTACAAAACATTGTATTAATTGATGTTAGAGAGACATTG
GAAATTCTTGATATTGAAAAATTCTAGAGTTCATCAATATACCATTAGATGAGATAGGTCAAGCTCATATGAACCCAGGA
TATTTCAAAGAGAAGTACAATAAAGTAAAACCATACGAATCTGACAGTTTAGTGTTTTCTTGTCTAGCTAGATAAGAAAG
AAACGAGAAGACTTTGAACACAGCAATGTCTTTGTGCTTTAATAGTGCTCAACAATATGCTGGAGATTGGAAGAAGTGGG
CAACATGGGAATTTTCAGAGAATAAACAAAGAAGT

Alignment

ORF - retro_ecab_791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.67 %
• Parental protein coverage: 91.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AILGSADSALWGVKSIKGSCHNFCTA-VSEDVTYEELKNRLNSK-SIMLIDVREKWEILE-YGKIPGSVN
          A.L.S.D..L....SIKGSC.NF........V.Y.E.KN.LN.K..I.LIDVRE..EIL..Y.KI....N
Retrocopy AALWSLDAMLKDLRSIKGSCQNFSIS<LPKEVIYQEPKNLLNYK<NIVLIDVRETLEILD<Y*KILEFIN

Parental  IPLAEVSEALQMNPKAFHEKYNEAKPSRSDRLVFSCVAG-VRSKKALDTAISLGFSSAQHYAGGWKEWAT
          IPL.E...A..MNP..F.EKYN..KP..SD.LVFSC.A...R..K.L.TA.SL.F.SAQ.YAG.WK.WAT
Retrocopy IPLDEIGQA-HMNPGYFKEKYNKVKPYESDSLVFSCLAR*ERNEKTLNTAMSLCFNSAQQYAGDWKKWAT

Parental  YECSEKKERN
          .E.SE.K.R.
Retrocopy WEFSENKQRS

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	5.55 RPM
SRP021940_cerebellum	0.00 RPM	18.80 RPM
SRP021940_embryo	0.00 RPM	6.11 RPM
SRP021940_placental_villous	0.00 RPM	16.26 RPM
SRP021940_synovial_membrane	0.00 RPM	7.11 RPM
SRP021940_testis	0.00 RPM	2.30 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_791 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_791 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_791 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_606

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008959	1 retrocopy	retro_amel_1055,
Bos taurus	ENSBTAG00000038931	1 retrocopy	retro_btau_1353,
Canis familiaris	ENSCAFG00000030791	1 retrocopy	retro_cfam_606,
Callithrix jacchus	ENSCJAG00000031571	1 retrocopy	retro_cjac_1967,
Equus caballus	ENSECAG00000000506	1 retrocopy	retro_ecab_631,
Equus caballus	ENSECAG00000024361	1 retrocopy	retro_ecab_791 ,
Gorilla gorilla	ENSGGOG00000022586	1 retrocopy	retro_ggor_1345,
Otolemur garnettii	ENSOGAG00000025707	2 retrocopies	retro_ogar_2601, retro_ogar_527,