RetrogeneDB ID: retro_ecab_661

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:440229..440775(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HOMER2
• Ensembl ID: ENSECAG00000023619
• Aliases: None
• Description: homer homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17513]

Sequence

>retro_ecab_661
TCTGTGACATAGAGTGCTGCCAATGTGAAGAAATAGGAGAATAAGCTGCAGACCCTGCAGAAGAGCAATGTCCGGCTGAC
CACGGCACTGCAGGAGTCAGTGGCCAGCATGGAGCAGTGGAAGAGGAAGTTCTCTATCTGCCCTGAAGAGAATGACTGGC
TGTGGAACAATCCTGAGGAGTTGGAAGAACAATGCAGAGAGATAACAAAGAGAAGGAGACAAATAGTCAGTTAAAGAGAA
GAAATGAGGAGCTGGAGTCAGAACACTGAGAAAAGAAGATAGTTAAAAGACCTCCAAAAACAAAGTAAACTCAGACCTCA
GCTCATGTCAGAGTGTGAATACATTTCTGAGCAGTTAGAGGCAGCAAAGAGAGATAATCAAAATCAGAGAGACAAAGTGC
TTTCTCTAAAGACAGACATTGAGGAAGGTAACTACTGACCATGCCGCTTGAAGGCAGAATTGAAGAACATCTTGAAGGTG
CTGGACGGGAAGATCAATGGCCTCCACAACTTCTGTGGAGGCCTCTGCAAGCTGGGCAAGGAAAGC

Alignment

ORF - retro_ecab_661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.02 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALTQSAANVKKWEVELQTLRESNARLTAALQESAASAEQWKRQFSVCRDENDRLRHKIDELEEQCSEINR
          ..T.SAANVKK.E..LQTL..SN.RLT.ALQES.AS.EQWKR.FS.C..END.L.....ELEEQC.EI..
Retrocopy SVT*SAANVKK*ENKLQTLQKSNVRLTTALQESVASMEQWKRKFSICPEENDWLWNNPEELEEQCREITK

Parental  EKEKNTQLKRRIEELESELREKETELKDLRKQSEIIPQLMSECEYVSEKLEAAERDNQNLEDKVRSLKTD
          ................S...EK...LKDL.KQS...PQLMSECEY.SE.LEAA.RDNQN..DKV.SLKTD
Retrocopy RRRQIVS*REEMRSW-SQNTEKRR*LKDLQKQSKLRPQLMSECEYISEQLEAAKRDNQNQRDKVLSLKTD

Parental  IEESKYRQRHLKVELKNFLEVLDGKIDDLHDFRRGLSKLGTDN
          IEE..Y....LK.ELKN.L.VLDGKI..LH.F..GL.KLG...
Retrocopy IEEGNY*PCRLKAELKNILKVLDGKINGLHNFCGGLCKLGKES

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	1.95 RPM
SRP021940_cerebellum	0.00 RPM	11.74 RPM
SRP021940_embryo	0.00 RPM	11.97 RPM
SRP021940_placental_villous	0.00 RPM	1.35 RPM
SRP021940_synovial_membrane	0.00 RPM	1.87 RPM
SRP021940_testis	0.00 RPM	11.57 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_661 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_661 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_661 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015884	3 retrocopies	retro_cjac_3556, retro_cjac_3614, retro_cjac_3871,
Cavia porcellus	ENSCPOG00000014688	1 retrocopy	retro_cpor_35,
Equus caballus	ENSECAG00000023619	3 retrocopies	retro_ecab_1046, retro_ecab_661 , retro_ecab_692,
Homo sapiens	ENSG00000103942	1 retrocopy	retro_hsap_1468,
Macaca mulatta	ENSMMUG00000008297	1 retrocopy	retro_mmul_2278,
Nomascus leucogenys	ENSNLEG00000010953	1 retrocopy	retro_nleu_3002,
Pongo abelii	ENSPPYG00000006735	5 retrocopies	retro_pabe_1209, retro_pabe_1210, retro_pabe_1217, retro_pabe_3566, retro_pabe_3568,