RetrogeneDB ID: retro_ecab_737

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:19496761..19497180(-)
• Located in intron of: ENSECAG00000000265

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC3
• Ensembl ID: ENSECAG00000024410
• Aliases: None
• Description: ER membrane protein complex subunit 3 [Source:HGNC Symbol;Acc:23999]

Sequence

>retro_ecab_737
GTGCTCGACTCCAGCAGGAGCCTCTGGGTGGTTTTGCCCATCTTTATCATCACTTCTTTGCAGGTATGAGCCACCACTGT
GGTCCACAGTGCTGCAGAGTGACAAGAAGCTCACCCGGGAGCAGGTATCTGACAGTTAAGTCTTAATTTGAAGCATAGTC
CTCAGGGAAAATGCAAATTATATTCCCAAATAGTTCTTCTTGACATGAAAATATTGCTTCAACAACCCAGAGGATAGATT
TTTCAAAAAAAAATGAAGCAAAAATAGTACGAACTTCTCCTATGACTGATCCCACTATGCTCACTGACATGATAAAAGGG
AGTGTACCAATCTTCCTCCCTATGATTCTTATTGGTGGATAGATCAACACGATATTCTCGGGCTTTGTCACAACCAAAGT
CCTATTTCCAATGACCCTG

Alignment

ORF - retro_ecab_737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 53.64 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLDSNIRLWVVLPIVIIT-FFVGMIRH-YVSILLQSDKKLTQEQVSDSQVLIRSRVLRENGKYIPKQSFL
          .LDS...LWVVLPI.IIT.FF.GM..H...S..LQSDKKLT.EQVSDS.VLI.S.VLREN..YIPK..FL
Retrocopy VLDSSRSLWVVLPIFIIT<FFAGMSHH<LWSTVLQSDKKLTREQVSDS*VLI*SIVLRENANYIPK*FFL

Parental  TRKYYFNNPEDGFFKKT-KRKVVPPSPMTDPTMLTDMMKGNVTNVLPMILIGGWINMTFSGFVTTKVPFP
          T.KY.FNNPED.FF......K.V..SPMTDPTMLTDM.KG.V...LPMILIGG.IN..FSGFVTTKV.FP
Retrocopy T*KYCFNNPEDRFFXXX>EAKIVRTSPMTDPTMLTDMIKGSVPIFLPMILIGG*INTIFSGFVTTKVLFP

Parental  LTL
          .TL
Retrocopy MTL

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	30.58 RPM
SRP021940_cerebellum	0.00 RPM	46.95 RPM
SRP021940_embryo	0.00 RPM	31.58 RPM
SRP021940_placental_villous	0.00 RPM	69.81 RPM
SRP021940_synovial_membrane	0.00 RPM	28.44 RPM
SRP021940_testis	0.00 RPM	105.70 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_737 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_737 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_737 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005202	1 retrocopy	retro_cfam_730,
Callithrix jacchus	ENSCJAG00000037305	1 retrocopy	retro_cjac_3209,
Equus caballus	ENSECAG00000024410	1 retrocopy	retro_ecab_737 ,
Felis catus	ENSFCAG00000024898	2 retrocopies	retro_fcat_1932, retro_fcat_2002,
Microcebus murinus	ENSMICG00000002333	2 retrocopies	retro_mmur_439, retro_mmur_707,
Mustela putorius furo	ENSMPUG00000017149	1 retrocopy	retro_mputfur_456,
Pteropus vampyrus	ENSPVAG00000012615	3 retrocopies	retro_pvam_1260, retro_pvam_1278, retro_pvam_1439,
Tursiops truncatus	ENSTTRG00000007554	2 retrocopies	retro_ttru_1311, retro_ttru_285,
Vicugna pacos	ENSVPAG00000003247	2 retrocopies	retro_vpac_308, retro_vpac_461,