RetrogeneDB ID: retro_ecab_174

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:78145488..78145991(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf78
• Ensembl ID: ENSECAG00000018958
• Aliases: None
• Description: chromosome 9 open reading frame 78 [Source:HGNC Symbol;Acc:24932]

Sequence

>retro_ecab_174
CAGATGAAAACAGGTGGTATGGACGACATGAGGAGACTGAAGGACAGAGGCACAGAAAAGATCAGTAGAGAGGAAGACCC
CACCTGAGGACATCATTTTGTGCAGAAACCAACTGACGGCACAAGGCTGCACACATGATGAAGAGTGTTAAGATGAAGGT
GAAGAGGAAAGGGATCATAGAACACAGGAGCAGAAAATCAACTCCAAGAATGCAGATCATATGCCTATGAACTTGTAGAA
AACCTCCATGCTTCCTCAGCAAAGAAGACTGTAGAATATCTTCCAAGTGGATGCTGAGCAGCATCCCCATTGTAGGCCTC
CACATGATGCTAAAATAAGAAATATTTTCATGGAGGATGCTAAGGCTCAGCTGCTGGCAGAGCAGCAGAACAGAAGAAAG
ACAGTGAGACATTCTGTGGGTCTACTATTGTGGCTGTGAGTTATGGGCAGCAAACCAATCTTATCACCAGGTTTTCAATG
CCCCTAGACGGAGAACAAAGGAT

Alignment

ORF - retro_ecab_174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.66 %
• Parental protein coverage: 59.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  QMKTGGMVDMKKLKERGKDKISEEED-LHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEH-EEQKV
          QMKTGGM.DM..LK.RG..KIS.EED..HL.TSF.AETN.R...A.MMK.......KRKGI.EH..EQK.
Retrocopy QMKTGGMDDMRRLKDRGTEKISREED<PHLRTSFCAETN*RHKAAHMMKSVKMKV-KRKGIIEH<QEQKI

Parental  KPKNAE-DCLYELPENIRVSSAKKTEEML-SNQMLSGIPEVDLGI-DAKIKNIISTEDAKARLLAEQQNK
          ..KNA.....YEL.EN...SSAKKT.E.L.S..MLS.IP.V.L...DAKI.NI...EDAKA.LLAEQQN.
Retrocopy NSKNAD<SYAYELVENLHASSAKKTVEYL<SKWMLSSIPIVGLHM<DAKIRNIF-MEDAKAQLLAEQQNR

Parental  -KKDSETSFVPTNMAVNYVQH-NRFYHEELNAPIRRNKE
          .KKDSET....T..AV.Y.Q..N..YH...NAP.RR.K.
Retrocopy <KKDSETFCGSTIVAVSYGQQ<NQSYHQVFNAPRRRTKD

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	22.14 RPM
SRP021940_cerebellum	0.00 RPM	34.79 RPM
SRP021940_embryo	0.00 RPM	38.36 RPM
SRP021940_placental_villous	0.00 RPM	27.38 RPM
SRP021940_synovial_membrane	0.00 RPM	26.88 RPM
SRP021940_testis	0.00 RPM	51.03 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_174 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_174 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_320
Pan troglodytes	retro_ptro_258
Callithrix jacchus	retro_cjac_1757
Bos taurus	retro_btau_1138

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020307	1 retrocopy	retro_btau_1138,
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Cavia porcellus	ENSCPOG00000009285	1 retrocopy	retro_cpor_712,
Equus caballus	ENSECAG00000018958	1 retrocopy	retro_ecab_174 ,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Microcebus murinus	ENSMICG00000009596	1 retrocopy	retro_mmur_1466,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Mus musculus	ENSMUSG00000026851	1 retrocopy	retro_mmus_2978,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,
Ictidomys tridecemlineatus	ENSSTOG00000020630	1 retrocopy	retro_itri_1783,
Tupaia belangeri	ENSTBEG00000013115	1 retrocopy	retro_tbel_514,