RetrogeneDB ID: retro_ecab_993

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:40900171..40900877(-)
• Located in intron of: ENSECAG00000018963

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000016527
• Aliases: None
• Description: None

Sequence

>retro_ecab_993
CAACAAATAGTAAATATAAGAAAGAAACAATCAGAGCTAAAGAATACAATAATGGAAATGAAAAATACACTAGGGGGAAT
CAACAGCAGATTAGATGATAAAGTACGAATCAGCAGTCTGGAAGACAAAGTAGTGGAAATCACCAATCAGAATATCAAAA
AGAAAATAGAATTTTAAAAAATGAGGATACTTTAAGGGACCTCTGGGACAACATCAAGCATAATAACATTCTCATTATTG
GTGTCCCAGAAGGAGAAGAGAGAGAGAAAGGGGCGGAAAATTTATTTGAAGAAATAATGGCTGAAAACTTCTCTAACTTA
GGGAAGGAAACAGACATCCAGATCCAGGAGAGTTCCAGACAAGATGAACCCAAAGAGATTCACACTAAGATATATTATAA
TTAAATTGGCAAAAGTTAAAGATAAAGAGAGAATCTTAAAGTCAGTAAGAGAAAAACGAGTCACATACAAAGGAACCTCC
CTAAGACTATAAGTTAATTTTTCAGCAGAAACTTTGCAGGCAAGAAGGGAGTGTCATGATATATTTAAAGTGCTGAAGGG
AAAAAAACTTACAACCAAGAATACTCTGCCCAACAAGGTTATCATTCAGGATTGAAAGAGACATAAAGAGTTTCCCAGAC
AAGCAAAAACTAAAGGAGTTCATCACCACTAAACTGGCCTTACAAGAAATGTTAAAGGGTTTTCTT

Alignment

ORF - retro_ecab_993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.09 %
• Parental protein coverage: 86.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KELENIKKNQSKNKHRLKQKTTHQLGKNICKDSIAQERTNKLDKRLEEIT-QADQIKEKRIKKNEDGLRD
          ....NI.K.QS..K...........G.N...D.....R...L.....EIT.Q....KE.RI.KNED.LRD
Retrocopy QQIVNIRKKQSELKNTIMEMKNTLGGINSRLDD--KVRISSLEDKVVEIT<QSEYQKENRILKNEDTLRD

Parental  LWNNIKHTNIHIIDVPEGEERDKGAENLFGEIIAENFPNLR-RKYPGEAQRAPNKINPKRPTPRHIIIKM
          LW.NIKH.NI.II.VPEGEER.KGAENLF.EI.AENF.NL..RK......R.P.K.NPKR.T.R.IIIK.
Retrocopy LWDNIKHNNILIIGVPEGEEREKGAENLFEEIMAENFSNLG>RKQTSRSRRVPDKMNPKRFTLRYIIIKL

Parental  SKSKDKERILNALRERQQVTYKGNPIRLSANFSAETLETRREWHDILKVLKG-KNLQPRILYSARLSF-M
          .K.KDKERIL...RE...VTYKG...RL..NFSAETL..RRE.HDI.KVLKG.KNLQPRIL...RLSF..
Retrocopy AKVKDKERILKSVREKR-VTYKGTSLRL*VNFSAETLQARRECHDIFKVLKG>KNLQPRILCPTRLSFRI

Parental  EGEIE-FPDKQNLEEFITKKPALQEMLNGLI
          E..I..FPDKQ.L.EFIT.K.ALQEML.G..
Retrocopy ERDIKSFPDKQKLKEFITTKLALQEMLKGFL

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.31 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.36 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_993 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_993 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_993 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010030	21 retrocopies	retro_ecab_1021, retro_ecab_1023, retro_ecab_1035, retro_ecab_1071, retro_ecab_1089, retro_ecab_136, retro_ecab_182, retro_ecab_201, retro_ecab_281, retro_ecab_306, retro_ecab_486, retro_ecab_521, retro_ecab_537, retro_ecab_582, retro_ecab_590, retro_ecab_658, retro_ecab_670, retro_ecab_722, retro_ecab_786, retro_ecab_974, retro_ecab_996,
Equus caballus	ENSECAG00000016527	5 retrocopies	retro_ecab_214, retro_ecab_642, retro_ecab_879, retro_ecab_888, retro_ecab_993 ,
Equus caballus	ENSECAG00000020332	9 retrocopies	retro_ecab_1018, retro_ecab_117, retro_ecab_125, retro_ecab_346, retro_ecab_54, retro_ecab_604, retro_ecab_774, retro_ecab_775, retro_ecab_878,
Equus caballus	ENSECAG00000022034	4 retrocopies	retro_ecab_1039, retro_ecab_278, retro_ecab_821, retro_ecab_858,
Equus caballus	ENSECAG00000023806	15 retrocopies	retro_ecab_1040, retro_ecab_1050, retro_ecab_1073, retro_ecab_1077, retro_ecab_1108, retro_ecab_176, retro_ecab_241, retro_ecab_298, retro_ecab_339, retro_ecab_714, retro_ecab_778, retro_ecab_781, retro_ecab_852, retro_ecab_855, retro_ecab_953,