RetrogeneDB ID: retro_ecab_1116

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:61808743..61809077(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRB
• Ensembl ID: ENSECAG00000009780
• Aliases: None
• Description: ubiquinol-cytochrome c reductase binding protein [Source:HGNC Symbol;Acc:12582]

Sequence

>retro_ecab_1116
ATGGTGAGCAGGCCTGTCATTGCAGCATCAAGCCAGTGGCTGGAGGGTATTCAAAAATGGAATTACTATGCTGCTGGGTT
TAATAAACTGGGGTTAATGTGAGATGATACAATATATGAGGATGATGATGTAAGAGAAGACATAAAGAAGGCTTCCTGAG
AAATTTTATAATGACAGGGTGTTTCACACTAAAAGAGCACTGGATCTGACCATGAGGCAGCAGATCATGCCTAAAGACCA
GTGGACAAAATATGAGGAGGATATATTCTACCTTGAACCATATCTGAAAGAGTTTATTTGGGAAAGAAAAGAGAGAGAAG
AATGGGCAAAGAAA

Alignment

ORF - retro_ecab_1116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASRPTVAASSRWLEGIRKWYYNAAGFNKLGLMRDDTIHENDDVKEAI-RRLPENLYNDRVFRIKRALDL
          M.SRP..AASS.WLEGI.KW.Y.AAGFNKLGLM.DDTI.E.DDV.E.I.RRLPE..YNDRVF..KRALDL
Retrocopy MVSRPVIAASSQWLEGIQKWNYYAAGFNKLGLM*DDTIYEDDDVREDI>RRLPEKFYNDRVFHTKRALDL

Parental  TMRQQILPKEQWTKYEEDKFYLEPYLKEVIRERKEREEWAKK
          TMRQQI.PK.QWTKYEED.FYLEPYLKE.I.ERKEREEWAKK
Retrocopy TMRQQIMPKDQWTKYEEDIFYLEPYLKEFIWERKEREEWAKK

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	17.83 RPM
SRP021940_cerebellum	0.00 RPM	28.25 RPM
SRP021940_embryo	0.03 RPM	38.64 RPM
SRP021940_placental_villous	0.00 RPM	41.28 RPM
SRP021940_synovial_membrane	0.00 RPM	16.14 RPM
SRP021940_testis	0.00 RPM	42.01 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1116 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001521	3 retrocopies	retro_btau_1641, retro_btau_374, retro_btau_417,
Choloepus hoffmanni	ENSCHOG00000007884	22 retrocopies	retro_chof_1256, retro_chof_1271, retro_chof_1468, retro_chof_1662, retro_chof_1888, retro_chof_2017, retro_chof_2170, retro_chof_2332, retro_chof_2528, retro_chof_2536, retro_chof_2554, retro_chof_257, retro_chof_2684, retro_chof_394, retro_chof_524, retro_chof_599, retro_chof_635, retro_chof_654, retro_chof_699, retro_chof_766, retro_chof_773, retro_chof_975,
Equus caballus	ENSECAG00000009780	1 retrocopy	retro_ecab_1116 ,
Latimeria chalumnae	ENSLACG00000004465	1 retrocopy	retro_lcha_127,
Loxodonta africana	ENSLAFG00000002542	1 retrocopy	retro_lafr_727,
Nomascus leucogenys	ENSNLEG00000026670	1 retrocopy	retro_nleu_1357,
Pteropus vampyrus	ENSPVAG00000012321	1 retrocopy	retro_pvam_498,
Rattus norvegicus	ENSRNOG00000024967	1 retrocopy	retro_rnor_290,
Ictidomys tridecemlineatus	ENSSTOG00000008017	1 retrocopy	retro_itri_46,
Tupaia belangeri	ENSTBEG00000002453	28 retrocopies	retro_tbel_1046, retro_tbel_1268, retro_tbel_1357, retro_tbel_1568, retro_tbel_1583, retro_tbel_1656, retro_tbel_1688, retro_tbel_169, retro_tbel_1858, retro_tbel_2106, retro_tbel_2217, retro_tbel_248, retro_tbel_2675, retro_tbel_274, retro_tbel_2883, retro_tbel_2885, retro_tbel_2893, retro_tbel_2942, retro_tbel_3129, retro_tbel_3156, retro_tbel_3291, retro_tbel_3492, retro_tbel_3662, retro_tbel_4334, retro_tbel_4539, retro_tbel_457, retro_tbel_517, retro_tbel_784,
Tursiops truncatus	ENSTTRG00000007348	3 retrocopies	retro_ttru_1106, retro_ttru_501, retro_ttru_754,
Drosophila melanogaster	FBgn0030733	1 retrocopy	retro_dmel_22,