RetrogeneDB ID: retro_ecab_310

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:36275289..36275589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRIPT
• Ensembl ID: ENSECAG00000012342
• Aliases: None
• Description: cysteine-rich PDZ-binding protein [Source:HGNC Symbol;Acc:14312]

Sequence

>retro_ecab_310
ATGGTGTGCAAGAAGCGTGAAAAGAAAGTTGGAACTGTTATCATTCCAGATACATGGAAAGATGGTCCAAGGAATACCAC
AGAAGTAGTGGAAGAAAGCCGAATGAAAATAAAGCTTTGACTTCAAAAAGCAAATTTCGATCCATATGGAAAGAATAAGT
TCTCCACTTGCAGAATTTCTGAAAGTTCTGTACACCAGCCATGTTCTCATTACTTCCATGGCTGTGCCTACAAAAAGGGC
ATCTGTGCCATGTGTGGGGAAAAGGTTTCAGAGACCAAAAACTACAAGCAAATATCTGTC

Alignment

ORF - retro_ecab_310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVCEKCEKKLGTVITPDTWKDGARNTTE-SGGRKLNENKALTSKKARF-DPYGKNKFSTCRICKSSVHQP
          MVC.K.EKK.GTVI.PDTWKDG.RNTTE.S.GRK.NENKALTS.K..F.DPYGKNKFSTCRI..SSVHQP
Retrocopy MVCKKREKKVGTVIIPDTWKDGPRNTTE<SSGRKPNENKALTS-KSKF>DPYGKNKFSTCRISESSVHQP

Parental  GSHYCQGCAYKKGICAMCGKKVLDTKNYKQTSV
          .SHY..GCAYKKGICAMCG.KV..TKNYKQ.SV
Retrocopy CSHYFHGCAYKKGICAMCGEKVSETKNYKQISV

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	2.24 RPM
SRP021940_cerebellum	0.00 RPM	3.53 RPM
SRP021940_embryo	0.00 RPM	2.28 RPM
SRP021940_placental_villous	0.00 RPM	5.53 RPM
SRP021940_synovial_membrane	0.00 RPM	2.31 RPM
SRP021940_testis	0.00 RPM	2.43 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_310 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_310 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015723	2 retrocopies	retro_btau_315, retro_btau_523,
Canis familiaris	ENSCAFG00000002633	1 retrocopy	retro_cfam_1105,
Choloepus hoffmanni	ENSCHOG00000000556	7 retrocopies	retro_chof_1031, retro_chof_1059, retro_chof_1241, retro_chof_2093, retro_chof_235, retro_chof_634, retro_chof_956,
Cavia porcellus	ENSCPOG00000008081	1 retrocopy	retro_cpor_1128,
Dipodomys ordii	ENSDORG00000006085	1 retrocopy	retro_dord_788,
Equus caballus	ENSECAG00000012342	2 retrocopies	retro_ecab_310 , retro_ecab_366,
Felis catus	ENSFCAG00000015610	1 retrocopy	retro_fcat_1369,
Microcebus murinus	ENSMICG00000009133	1 retrocopy	retro_mmur_30,
Myotis lucifugus	ENSMLUG00000004193	2 retrocopies	retro_mluc_1480, retro_mluc_2080,
Macaca mulatta	ENSMMUG00000005388	1 retrocopy	retro_mmul_1191,
Monodelphis domestica	ENSMODG00000000973	1 retrocopy	retro_mdom_532,
Otolemur garnettii	ENSOGAG00000008089	6 retrocopies	retro_ogar_1206, retro_ogar_1967, retro_ogar_2609, retro_ogar_2734, retro_ogar_3132, retro_ogar_984,
Rattus norvegicus	ENSRNOG00000015215	1 retrocopy	retro_rnor_2485,
Tarsius syrichta	ENSTSYG00000002853	2 retrocopies	retro_tsyr_1596, retro_tsyr_85,
Vicugna pacos	ENSVPAG00000000315	1 retrocopy	retro_vpac_417,