RetrogeneDB ID: retro_ecab_648

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 25:17556004..17556331(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000005976
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SH3BGRL
• Ensembl ID: ENSECAG00000012612
• Aliases: None
• Description: SH3 domain binding glutamic acid-rich protein like [Source:HGNC Symbol;Acc:10823]

Sequence

>retro_ecab_648
ATGGTGACCCGTGTGTATATTTCATCTTCCTCTGGCTGTCTGGCGATTAAGAAGAAACAGCAAGATGTGCTTGGTTTCTT
AGAAGCTAACAAAATAGGATTTGAAGAAGAAGAGATTGCATCCAATGAAGAAAATTGGAAGTGGATGAGAGAAAATGTAC
CTGAAAACAGTCAACCAGCCACAGGGTACCCCCTGCCACCTCAGATTTTCACTGAAAGCCAGTACCGTGGGGACCATGAG
GACTTCTTTGAAGCCAGAGAAAACAGTGCAGTGTATTCCTTTTTAGGCTCGACAGGCCCACCTGGTTCAAAGGAAACAGA
AGCTCAG

Alignment

ORF - retro_ecab_648 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.49 %
• Parental protein coverage: 95.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVIRVYIASSSGSTAIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGYPLPPQIF
          MV.RVYI.SSSG..AIKKKQQDVLGFLEANKIGFEE..IA.NEEN.KWMRENVPENS.PATGYPLPPQIF
Retrocopy MVTRVYISSSSGCLAIKKKQQDVLGFLEANKIGFEEEEIASNEENWKWMRENVPENSQPATGYPLPPQIF

Parental  NESQYRGDYDAFFEARENNAVYAFLGLTAPPGSKEAEAQ
          .ESQYRGD...FFEAREN.AVY.FLG.T.PPGSKE.EAQ
Retrocopy TESQYRGDHEDFFEARENSAVYSFLGSTGPPGSKETEAQ

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	15.94 RPM
SRP021940_cerebellum	0.00 RPM	2.13 RPM
SRP021940_embryo	0.03 RPM	38.95 RPM
SRP021940_placental_villous	0.00 RPM	24.97 RPM
SRP021940_synovial_membrane	0.00 RPM	27.86 RPM
SRP021940_testis	0.00 RPM	3.58 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_648 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_648 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004130	1 retrocopy	retro_chof_647,
Callithrix jacchus	ENSCJAG00000003568	2 retrocopies	retro_cjac_1102, retro_cjac_140,
Cavia porcellus	ENSCPOG00000012267	3 retrocopies	retro_cpor_1172, retro_cpor_244, retro_cpor_844,
Dipodomys ordii	ENSDORG00000011106	2 retrocopies	retro_dord_199, retro_dord_588,
Equus caballus	ENSECAG00000012612	1 retrocopy	retro_ecab_648 ,
Ictidomys tridecemlineatus	ENSSTOG00000013216	1 retrocopy	retro_itri_1152,