RetrogeneDB ID: retro_ecab_987

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:23792534..23792849(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA2
• Ensembl ID: ENSECAG00000015007
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 2 [Source:HGNC Symbol;Acc:28006]

Sequence

>retro_ecab_987
ATGTTCCAGAAAGCCGACTCTGATCTGGATACACTCAGGACAGGGTGGATATGAAATCAACACTAATCACCCTGATTTGG
CAGGGGAGAAACATCCAATTACACTCCTAAAGGAATCAGCAGCCAAAAGCCTCGATGTCAGACTTTGCACACACGTGTGA
AGCCAGCTGCTGCTGAGCAGAAAGGCTGAGCGCCTCATCAGTGCTCTTCTGAATGAGACTATGACCGGGACACAAGAACC
ACACAGACACACAGACCTGGAACTGGCACCACTGACTGAAGAAGAGAAGACCGCCCCAGAGCAACTAAATCTCAC

Alignment

ORF - retro_ecab_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.27 %
• Parental protein coverage: 96.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFQKADSDLD-YIQYRLE-YEIKTNHPDSAGEKNPVTLLKELSAIKSRYQTLQARFKPVAIEQKETKSRI
          MFQKADSDLD.Y.Q.R...YEI.TNHPD.AGEK.P.TLLKE.SA.KS....L.................I
Retrocopy MFQKADSDLD<YTQDRVD<YEINTNHPDLAGEKHPITLLKE-SAAKSLDVRLCTHV*SQLLLSRKAERLI

Parental  CATFNKTMAMIQELQKQTDLELSPLTEEEKTAAEQL-KSH
          .A..N.TM...QE....TDLEL.PLTEEEKTA.EQL.KSH
Retrocopy SALLNETMTGTQEPHRHTDLELAPLTEEEKTAPEQL<KSH

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	1.48 RPM
SRP021940_cerebellum	0.00 RPM	4.62 RPM
SRP021940_embryo	0.41 RPM	16.55 RPM
SRP021940_placental_villous	0.10 RPM	3.27 RPM
SRP021940_synovial_membrane	0.19 RPM	3.07 RPM
SRP021940_testis	0.00 RPM	5.75 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_987 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_987 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021680	2 retrocopies	retro_btau_310, retro_btau_945,
Canis familiaris	ENSCAFG00000029233	1 retrocopy	retro_cfam_766,
Cavia porcellus	ENSCPOG00000006051	1 retrocopy	retro_cpor_542,
Dipodomys ordii	ENSDORG00000010768	2 retrocopies	retro_dord_103, retro_dord_281,
Equus caballus	ENSECAG00000015007	1 retrocopy	retro_ecab_987 ,
Felis catus	ENSFCAG00000022802	1 retrocopy	retro_fcat_1111,
Homo sapiens	ENSG00000182628	1 retrocopy	retro_hsap_4214,
Loxodonta africana	ENSLAFG00000003405	1 retrocopy	retro_lafr_1215,
Myotis lucifugus	ENSMLUG00000010942	1 retrocopy	retro_mluc_83,
Monodelphis domestica	ENSMODG00000014619	1 retrocopy	retro_mdom_347,
Mustela putorius furo	ENSMPUG00000015241	1 retrocopy	retro_mputfur_1435,
Mus musculus	ENSMUSG00000020492	2 retrocopies	retro_mmus_370, retro_mmus_778,
Otolemur garnettii	ENSOGAG00000026072	4 retrocopies	retro_ogar_1882, retro_ogar_2937, retro_ogar_3032, retro_ogar_907,
Rattus norvegicus	ENSRNOG00000025981	3 retrocopies	retro_rnor_1606, retro_rnor_523, retro_rnor_733,
Sorex araneus	ENSSARG00000011128	2 retrocopies	retro_sara_60, retro_sara_662,
Ictidomys tridecemlineatus	ENSSTOG00000024169	4 retrocopies	retro_itri_1115, retro_itri_1275, retro_itri_1434, retro_itri_725,
Tarsius syrichta	ENSTSYG00000006158	3 retrocopies	retro_tsyr_1620, retro_tsyr_2034, retro_tsyr_748,
Tursiops truncatus	ENSTTRG00000017196	1 retrocopy	retro_ttru_143,