RetrogeneDB ID: retro_ecab_759

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 30:29886197..29886926(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANXA2
• Ensembl ID: ENSECAG00000012670
• Aliases: None
• Description: annexin A2 [Source:RefSeq peptide;Acc:NP_001116852]

Sequence

>retro_ecab_759
GGCCGCCTGGAGATGGTGATCGGGGGCCTACTGAAAATACCCACTCGGTGTGACGCTTCCAAGCTGAAAGCCTCCATGAA
GGGGCTGGAGACTGATGAGGACCCCTCACTGAGATCCTGCTCAAGGACCAACCAGGAGCTTCAGGCAACTAACAGAGCCC
ACAATGAAAGGTACAAGACTGATCTGAGAAGGACATTGTTTCTGATACATCTGGTGACTCCCACAAGCTGATGGCTGCCC
TCACACAGCGCAGAAGAGCAGAGGAAGGCTCTGTCATTGATTAAGAACTGAGTGACCAAGATGCTCAGGATCGCCACGAT
GCTGGAGAGAAAGGAAAGGAACTGATGTTCCCAAATGGACCAGCATCATGACCGGGCAGAGTGTCTGTCATCTCCAGAAA
GTACTTGAAAGATACAAGAGCCACAGCCCTATGACGTGTTAGGCAGCATCCAGAAGGAGGTCAAAGGACACCCGGAGAAT
GCTTCCCTGGACCTGGTCCAGTGTATTCAGAATAAGCCCCCGTATTTTGCCAACTGACTATACGACTCCACGAAGGGCAA
GTGGTCACGTGATAAGGTCCTGATCAGAATCACGGCCTCCCACAGTGAAGTGGACATGTTGAAAATTAGGTCTGAATTCA
TGAGAAAGTACAGCAAGTCTGTGTCCTACCACATCCAGCAAGACACCACAGGTGACCGCCAGAAGGTGCTGCTGTGTGGT
TGGGATGAC

Alignment

ORF - retro_ecab_759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.4 %
• Parental protein coverage: 72.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDL-EKDIVS
          G.LE.VI.GLLK.P...DAS.LKASMKGL.TDED......CSRTNQELQ..NR...E.YKTDL.EKDIVS
Retrocopy GRLEMVIGGLLKIPTRCDASKLKASMKGLETDEDPSLRS-CSRTNQELQATNRAHNERYKTDL<EKDIVS

Parental  DTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVK-RKGTDVPKWISIMTERSVCHLQKVFE
          DTSGD..KLM.AL...RRAE.GSVID.EL.DQDA.D..DAG.K.RKGTDVPKW.SIMT..SVCHLQKV.E
Retrocopy DTSGDSHKLMAALTQRRRAEEGSVID*ELSDQDAQDRHDAGEK<RKGTDVPKWTSIMTGQSVCHLQKVLE

Parental  RYKSYSP-YDMLESIKKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVD
          RYKS.SP.YD.L.SI.KEVKG..ENA.L.LVQCIQNKP.YFA..LYDS.KGK..RDKVLIRI..S.SEVD
Retrocopy RYKSHSP<YDVLGSIQKEVKGHPENASLDLVQCIQNKPPYFAN*LYDSTKGKWSRDKVLIRITASHSEVD

Parental  MLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
          MLKIRSEF.RKY.KS..Y.IQQDT.GD.QK.L..LCG.DD
Retrocopy MLKIRSEFMRKYSKSVSYHIQQDTTGDRQKVL--LCGWDD

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	243.32 RPM
SRP021940_cerebellum	0.00 RPM	20.67 RPM
SRP021940_embryo	0.03 RPM	220.82 RPM
SRP021940_placental_villous	0.00 RPM	1183.44 RPM
SRP021940_synovial_membrane	0.03 RPM	736.59 RPM
SRP021940_testis	0.00 RPM	39.64 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_759 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_759 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008055	2 retrocopies	retro_amel_1531, retro_amel_1836,
Bos taurus	ENSBTAG00000009615	2 retrocopies	retro_btau_634, retro_btau_985,
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Equus caballus	ENSECAG00000012670	1 retrocopy	retro_ecab_759 ,
Felis catus	ENSFCAG00000007862	2 retrocopies	retro_fcat_594, retro_fcat_709,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106, retro_ptro_81,
Tursiops truncatus	ENSTTRG00000007705	1 retrocopy	retro_ttru_1725,