RetrogeneDB ID: retro_ecab_327

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:29518722..29519302(+)
• Located in intron of: ENSECAG00000007763

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000018840
• Aliases: None
• Description: None

Sequence

>retro_ecab_327
AATGTAGAAATTCTACGGATGGAAGAGGAGACAGAACTAAGATTGTAAAAAAAGAAGAAATTCTTTGAGAAATATCTGAT
TCAATTAGGAAAAGCAACATAAGGATTATATATCCCAGAGGAAGAAGAGAGGGAGAAAGGAGCAGAGAGTTTGTTCAAAG
AACTAATTGCTGAGAACGTCCCAAACATGGGGATGGTTTCAGATTTACAGATAAACGAAGTTAACCGAAGGCCTACCTTT
ATCAACATAAAAAGACCCTTTCCAAGGCATATAATATTGAAAATGGCAAAAGTCTGGGATAAAGAAAGAATATCAGGAGC
AGCAAGGCAGGAGAAAATAACTTACAAAGGAAACCCTATGAGGCTTTCAGCAGATTGCTCAGCAGAACCTACAAGCTAGG
AGAGAATGGAACGATATATTCAACATACTGAAAGACAAAAACTTTCTGCCGAGAACACTCCATCCAGCCAAACTTTCCTT
CAGATACGATGGAGAAATAAAAGTTTTCTCAGATAAACAAAAGCTGAGGGAGTTCATCGCCACTAGACTTCCCCTACAAG
AAATAATTCAAGATGTCCTC

Alignment

ORF - retro_ecab_327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.61 %
• Parental protein coverage: 97.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NTEMLKMEEERELRLKRSEDIFQEIYNPIRKRNIRIISIPTGEERQNRRESLFKEIITENFLNLGKGLEI
          N.E.L.MEEE.ELRL......F........K.......IP..EER....ESLFKE.I.EN..N.G.....
Retrocopy NVEILRMEEETELRL*KKKKFFEKYLIQLGKAT*GLY-IPEEEEREKGAESLFKELIAENVPNMGMVSDL

Parental  QVKEANRTPNYINVERPSPRHILVKLAKLVMKEYIMAEAARQKKITYKGSPIRLSADFS-QTVQTRREWN
          Q..E.NR.P..IN..RP.PRHI..K.AK...KE.I...AARQ.KITYKG.P.RLSAD.S.Q..Q.RREWN
Retrocopy QINEVNRRPTFINIKRPFPRHIILKMAKVWDKERISG-AARQEKITYKGNPMRLSADCS>QNLQARREWN

Parental  DIIKILKYKNYPPRILYPVKLSFRYGREIKAFQDKQKLREFITTRPPLQEMMKTAL
          DI..ILK.KN..PR.L.P.KLSFRY..EIK.F.DKQKLREFI.TR.PLQE.....L
Retrocopy DIFNILKDKNFLPRTLHPAKLSFRYDGEIKVFSDKQKLREFIATRLPLQEIIQDVL

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_327 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_327 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000018840	28 retrocopies	retro_ecab_1000, retro_ecab_1011, retro_ecab_1045, retro_ecab_1062, retro_ecab_1076, retro_ecab_221, retro_ecab_243, retro_ecab_296, retro_ecab_322, retro_ecab_327 , retro_ecab_424, retro_ecab_482, retro_ecab_498, retro_ecab_523, retro_ecab_545, retro_ecab_564, retro_ecab_571, retro_ecab_663, retro_ecab_718, retro_ecab_742, retro_ecab_763, retro_ecab_787, retro_ecab_790, retro_ecab_824, retro_ecab_902, retro_ecab_908, retro_ecab_928, retro_ecab_929,