RetrogeneDB ID: retro_ecab_176

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:85331790..85332625(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000012809
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ecab_176
ATGAGGAGACAAAGAATATATTCTAAGCAAGGGAACAAGACAAAGCCCCAGAAAAAGTGCTAAATGAAACAAATAAATAG
TCTACCTGAAAAAGAGTTCAAGCAAAAAGTCATAAGGATGCTCACTGATCTTTGCAGAAGAATGGATGAACACAGTGAGA
GCATCAACAAAATATTAAAAAATATAAAAAAGCACCAATCAGAAATGAAGAATACAATACTGGAAATGAAAAATTCACTA
GAAGAACTCAATAGTAGAGTAGATGATACAGAAGAATGGATCAGTGAGCTGGATGAAAGACTAGAGGAAATCATCCAAGC
TGAACAGATAAAAAAGAATTAAAAAGAATGAGAACAAGCTAGGGGTACTCTGGGACAACATCAAGTGCACTAACATGCAT
ATTATGGTGTCTCAGAAGGAGAGAAGAGAGAGACAAAGGGGCAGAGAATCTATTTGAAGACATAGTAGCTGAAAACTTTT
TAACCTAAGGAAGGAAACAGCCATCTAGGTCCTGGAGGCATAGAGAGCACCAAACAAGATAAACTCAAAGAGGCCCACAC
CAAGACACATTATAATTAAAATGTCCAAAATTAAAGTTAAAGAGACAATCCTAAAAGCTTCAAGAGAAAGGCAACAAGTG
ACATACAAAGGAAATCCCATAAGGCTTTCAGCTGACTTCTCAGAGAAACTTTACGGCACAGAAGGGAGTGGCATGATATA
TTTAAAGTCCTGAAAGGAAAAAAATCTACAGCCAAGAATATTCTACCCAGCCAGGTTATCATTCAGAATGGAAGGAGAGA
GAAAACGTTTCCCAGACAAGCAAAAATTAAAGGAG

Alignment

ORF - retro_ecab_176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MRRQRNMFHARVQDKTPEKELNETQRDNLPDKEFKQKGIRMLIDLGRRMDKHSENVNKELENIKKSQSEM
          MRRQR...........P.K.....Q...LP.KEFKQK.IRML.DL.RRMD.HSE..N.........QSEM
Retrocopy MRRQR-IYSKQGNKTKPQKKC*MKQINSLPEKEFKQKVIRMLTDLCRRMDEHSESINXXXXXXXXHQSEM

Parental  KSTILKMKNSLEGLNSRVDDTEEWIKKLDEKLEEI-SQVNQVKEKTILKNDSKIKELWDNIKHANIRII-
          K.TIL.MKNSLE.LNSRVDDTEEWI..LDE.LEEI.S..N..K...I.KN..K...LWDNIK..N..I..
Retrocopy KNTILEMKNSLEELNSRVDDTEEWISELDERLEEI>SKLNR*KR--IKKNENKLGVLWDNIKCTNMHIM<

Parental  SVPGGEERH-KGE-ENLFEEIIDENFP-NLRKETDIQVQEEQRAPNKSSPKRPTPIHIIIKMSKIKDKER
          .V..GE.R..KG..ENLFE.I..ENF..NLRKET.I.V.E..RAPNK...KRPTP.HIIIKMSKIK.KE.
Retrocopy GVSEGEKRETKGQ<ENLFEDIVAENFL<NLRKETAI*VLEA*RAPNKINSKRPTPRHIIIKMSKIKVKET

Parental  ILKAARERPEVTYKGKPIRLSADFS-AETLQATREWHDIFKVLKG-KNLQPRIFYPSRSSFRMEGEIKRF
          ILKA.RER..VTYKG.PIRLSADFS..ETL...REWHDIFKVLKG.KNLQPRIFYP.R.SFRMEGE.KRF
Retrocopy ILKASRERQQVTYKGNPIRLSADFS<RETLRHRREWHDIFKVLKG>KNLQPRIFYPARLSFRMEGERKRF

Parental  PDKQNVKE
          PDKQ..KE
Retrocopy PDKQKLKE

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_176 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_176 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,