RetrogeneDB ID: retro_ecab_339

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:77612321..77613166(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000023806
• Aliases: None
• Description: None

Sequence

>retro_ecab_339
ATGAGGAGGAAAAGGAATACATTCCAAGCAAGGGAACAGGACAAAACCCCAGAAAAAGAACTAAATGAAACAGAAATAAG
CAGTCTACCTGACAAAGAGTTCAAACAAAAACTCATAAGGATGCTCACTGATATTGGGAGAAGAGTGGAGGAACACAGTG
AGAATGTCAACAAAGAATTGTAAAATATAAAAAAAGAACCAATTAAAAATGAAGAATACAATACTGGAAATGAAAAATTC
ACTAGATGGACTCAATAACAGAGTAGATGATACAGAAGAACAGATCAGTGAGCTGGATGAAAGACCACAGGAAATCATCC
AAGCTGAACAGACAAAAGAAAAAAGAATTAAAAAAGAATGAGAACAGTGAAAGGGGACTCTGGGACAATATTAAGCACAC
TAACATTAGTATTATAGGTGTCCCAGAAGGTGAAGAGAGAGACAAAGAGGCAGAGAATGTATTTGATGAAAGAGTGGCTG
AAAACTTTCCTAACCTAAGGAAGGAAAGAGACATCCAAATACAGGAAGCACAGAGAGCACCAAACAAGATGAACACCAAG
AGGCCCACATCAAGACACATTATAACTTAAATGTCCAAAACTAAAGATAAAGAGAAAATCCTAAATGAAACAAGGGAAAG
CCAACAAGTGAAATACAAAGCAAAGCCCCTAAAGCTATCAGCAGACTTCTCATCTGAAACCCTACAGGCTAGAAGAGAGT
GGCGTGACATATTTAAAGTGCTGAAAGGAAAAAACCTACAGCCAAGAATACTCTATCCAGAAAGGTTATAATTCAGAATG
GAAGGAGAGAGAAAGAGCTTCCCAGACAAGCAAAAATTAAAGGAG

Alignment

ORF - retro_ecab_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRRQRNMFHARVQDKTPEKELNETQRDNLPDKEFKQKGIRMLIDLGRRMDKHSENVNKELENI-KKSQSE
          MRR.RN.F.AR.QDKTPEKELNET....LPDKEFKQK.IRML.D.GRR...HSENVNKEL.NI.KK.Q..
Retrocopy MRRKRNTFQAREQDKTPEKELNETEISSLPDKEFKQKLIRMLTDIGRRVEEHSENVNKEL*NI>KKNQLK

Parental  MKSTILKMKNSLEGLNSRVDDTEEWIKKLDEKLEEI-SQVNQVKEKTILKNDSKIKELWDNIKHANIRII
          MK.TIL.MKNSL.GLN.RVDDTEE.I..LDE...EI.S..N.........N......LWDNIKH.NI.II
Retrocopy MKNTILEMKNSLDGLNNRVDDTEEQISELDERPQEI>SKLNRXXXXXXXXNENSERGLWDNIKHTNISII

Parental  SVPGGEERHKGEENLFEEIIDENFPNLRKETDIQVQEEQRAPNKSSPKRPTPIHIIIKMSKIKDKERILK
          .VP.GEER.K..EN.F.E...ENFPNLRKE.DIQ.QE.QRAPNK...KRPT..HII..MSK.KDKE.IL.
Retrocopy GVPEGEERDKEAENVFDERVAENFPNLRKERDIQIQEAQRAPNKMNTKRPTSRHIIT*MSKTKDKEKILN

Parental  AARERPEVTYKGKPIRLSADFSAETLQATREWHDIFKVLKGKNLQPRIFYPSRSSFRMEGEIKRFPDKQN
          ..RE...V.YK.KP..LSADFS.ETLQA.REW.DIFKVLKGKNLQPRI.YP.R..FRMEGE.K.FPDKQ.
Retrocopy ETRESQQVKYKAKPLKLSADFSSETLQARREWRDIFKVLKGKNLQPRILYPERL*FRMEGERKSFPDKQK

Parental  VKE
          .KE
Retrocopy LKE

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	0.12 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.28 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.08 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_339 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_339 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,