RetrogeneDB ID: retro_ecab_126

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:45311534..45312001(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000021553
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NOL12
• Ensembl ID: ENSECAG00000011050
• Aliases: None
• Description: nucleolar protein 12 [Source:HGNC Symbol;Acc:28585]

Sequence

>retro_ecab_126
GAGATCCAGCAGCGGCTCAAGCAGCAGCGCCACCAGGAATCCTTGCAGATGCTGTCCCAGAGAGAAGAGGTGCTGGGGGA
GGCAGCCCAGCTGGACTGGCTGCTGACGACAAACATAGGGTCTGAACAGTACGAACACGCCAACCGCACAGTCACCGCAA
GCATCATCCGCAACCTAGACCCCTCCAGGGTTGTCCAGCTGTTCCGACTGCCCCTGCCTGAGCAAGGGGCTAGGCACGGG
TCCGAGGATGCAGCATCATCCACGGGGAAGCCCACCAGCGCCTTTCCTAGGAAGTCCAGGGACCCCCTGCTATCCCAGGG
GACAGCCGCTCTCAAGGCTTCGCTACCCGCACAGTCGTAAAAAGGTCAAAGGCAACATCCGCCAAGGGGCCAGGACTCCA
CCATGAAGCCCTCAGTCCCAGTCCTACCAGCAAGACCCAGCGCAGCCAGCTGCCAGGTAAAGCCCGG

Alignment

ORF - retro_ecab_126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.7 %
• Parental protein coverage: 72.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEQKKLREERHQEYLKMLAEREEALEEADELDRLVTAKTESVQYDHPNHTVTVTTISDLDLSGA-RLLGL
          E.Q..L...RHQE.L.ML..REE.L.EA..LD.L.T....S.QY.H.N.TVT...I..LD.S....L..L
Retrocopy EIQQRLKQQRHQESLQMLSQREEVLGEAAQLDWLLTTNIGSEQYEHANRTVTASIIRNLDPSRVVQLFRL

Parental  PSAEQGAGHGSEEEAASVEKPTRALPRKSRDPLLSQRISSLTASLHAHSRKKVKRKHPRRAQDSTKKPP-
          P..EQGA.HGSE..A.S..KPT.A.PRKSRDPLLSQ....L.ASL.A.S.K...R.HP.R.QDST.KP..
Retrocopy PLPEQGARHGSEDAASSTGKPTSAFPRKSRDPLLSQGTAALKASLPAQS*KG-QRQHPPRGQDSTMKPS<

Parental  SATRTSKSQRRRLTGKAR
          S...TSK.QR..L.GKAR
Retrocopy SPSPTSKTQRSQLPGKAR

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	4.37 RPM
SRP021940_cerebellum	0.00 RPM	6.91 RPM
SRP021940_embryo	0.08 RPM	8.98 RPM
SRP021940_placental_villous	0.00 RPM	4.14 RPM
SRP021940_synovial_membrane	0.00 RPM	9.39 RPM
SRP021940_testis	0.00 RPM	17.14 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_126 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_126 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010139	1 retrocopy	retro_amel_672,
Callithrix jacchus	ENSCJAG00000012487	1 retrocopy	retro_cjac_538,
Equus caballus	ENSECAG00000011050	1 retrocopy	retro_ecab_126 ,
Felis catus	ENSFCAG00000004273	1 retrocopy	retro_fcat_757,
Oryctolagus cuniculus	ENSOCUG00000017013	1 retrocopy	retro_ocun_1698,
Otolemur garnettii	ENSOGAG00000008255	1 retrocopy	retro_ogar_2914,
Pteropus vampyrus	ENSPVAG00000010097	1 retrocopy	retro_pvam_1022,
Tupaia belangeri	ENSTBEG00000009745	1 retrocopy	retro_tbel_3215,
Tursiops truncatus	ENSTTRG00000004799	1 retrocopy	retro_ttru_1165,