RetrogeneDB ID: retro_ecab_662

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:2494602..2495036(-)
• Located in intron of: ENSECAG00000005320

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000025123
• Aliases: None
• Description: None

Sequence

>retro_ecab_662
GGTTACAGGCGGGTGTTTGAGGAGTACATGAGAGTTATTAGCCAGCGGTACCCGGACATCCGCATTGAAGGAGAGAATTA
CCTCCCTCAACCAATATATAGACACACAGCATCTTTCCTGTCAGTCTTCAAAATAGTATTAATTGGCTTAATTGTTGGCA
AGGATCCTTTTGCTTTCTTTGGCATGTAAGCTCCTAGCATCTGGCAGTGGCGCCAAGAAAATAAGGTCTGTGTGTGTATG
ATGGTCTTCTTCTTGAGCAACACGATTGAGGACCAGTGTATGTCAACAGGTGCATTTAGATAACTTTGAATGATGTACCT
GTGTGGTCTAAGCTGGAATCTGGTCACCTGCCATCCATGCAACAGCTTGTTCAAATTCTTGACAATGAAATGAAGCTGAG
TGTGCATATGGATCCAATCCCACATCATCGATCA

Alignment

ORF - retro_ecab_662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQ
          GYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRH.ASFLSVFK.VLIGL.IVGKDPFAFFGM.APSIWQ
Retrocopy GYRRVFEEYMRVISQRYPDIRIEGENYLPQPIYRHTASFLSVFKIVLIGL-IVGKDPFAFFGM*APSIWQ

Parental  WGQENKVYACMMVFFLSNMVENQCMSTGAFE-ITFNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMD
          W.QENKV..CMMVFFLSN..E.QCMSTGAF..IT.NDVPVWSKLESGHLPSMQQLVQILDNEMKL.VHMD
Retrocopy WRQENKVCVCMMVFFLSNTIEDQCMSTGAFR<ITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLSVHMD

Parental  PIPHHGS
          PIPHH.S
Retrocopy PIPHHRS

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	0.06 RPM	15.41 RPM
SRP021940_cerebellum	0.05 RPM	15.42 RPM
SRP021940_embryo	0.20 RPM	20.05 RPM
SRP021940_placental_villous	0.00 RPM	29.44 RPM
SRP021940_synovial_membrane	0.03 RPM	17.84 RPM
SRP021940_testis	0.00 RPM	26.79 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_662 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_662 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001394	2 retrocopies	retro_chof_1199, retro_chof_768,
Equus caballus	ENSECAG00000025123	2 retrocopies	retro_ecab_441, retro_ecab_662 ,
Homo sapiens	ENSG00000198843	2 retrocopies	retro_hsap_3384, retro_hsap_4126,
Gorilla gorilla	ENSGGOG00000028291	1 retrocopy	retro_ggor_1892,
Macropus eugenii	ENSMEUG00000014738	3 retrocopies	retro_meug_1766, retro_meug_1786, retro_meug_2036,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Mus musculus	ENSMUSG00000075700	1 retrocopy	retro_mmus_3111,
Nomascus leucogenys	ENSNLEG00000003284	2 retrocopies	retro_nleu_2473, retro_nleu_972,
Ochotona princeps	ENSOPRG00000014425	2 retrocopies	retro_opri_1052, retro_opri_584,
Pan troglodytes	ENSPTRG00000039581	1 retrocopy	retro_ptro_2804,
Rattus norvegicus	ENSRNOG00000013507	1 retrocopy	retro_rnor_2069,
Sarcophilus harrisii	ENSSHAG00000018506	1 retrocopy	retro_shar_629,
Tarsius syrichta	ENSTSYG00000007410	3 retrocopies	retro_tsyr_1515, retro_tsyr_167, retro_tsyr_46,