RetrogeneDB ID: retro_ecab_563

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:10036356..10037698(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMCC3
• Ensembl ID: ENSECAG00000011697
• Aliases: None
• Description: transmembrane and coiled-coil domain family 3 [Source:HGNC Symbol;Acc:29199]

Sequence

>retro_ecab_563
GTAGAGCGTCATGACATGAATACCCTAAGCCTGCCCCTCAACATACGCCGAGGGGGCTCAGACACCAACCTCAACTTCGA
CGTACCAGATGGCATCCTGGACTTCCACAAGGTCAAACTCAGCGCGGACAGCCTGAAGCAGAAAATCCTAAAGGTAACAG
AGCAGATAAAAATAGAGCAGACGTCCCGTGATGGGAACGTGGCGGAGTATCTGAAGCTGGTCAGCAGCGCGGACAAGCAG
CAGGCCGGCCGGATCAAGCAAGTCTTTGAGAAGAAGAATCAGAAGTCAGCTCACTCGATCGCCCAGCTGCAGAAGAAGTT
AGAAAAGTATCATAGAAAGCTCAAGGAGATCGAACAGAACGGAGCCTCCAAAAGCTCAAAGGACTTTTCCAAAGACCACC
TGGAGGACATCCAGCACTCTCTGAAAGATGCCCACGCCAAGTCTCGAACGGCGCCCGGCAACATGGAGAGCGGTAAATCG
GGCATGCCAGGGGTGTCCCTCACTCCCCCCGTGTTCGTCTTTAATAAGTCCAGGGAGTTTGCCAACCTGATCCGTAATAA
GTTTGGCAGCGCCGACAACATCGCTCACTTAAAAAATTCCTTAGAGGAGTTTAGGCCCAAGGCGAGTGCCAGGGTCTACG
GGGACAGCGCGACCATTGTGAACAAGCCCAAGTATGGCAGTGACGACGAGTGTTCAAGTGGCACCTCGGGTTCCACCGAC
AGTAATGGGAACCAGTCGTCCGGGCTGGTGGAGCCAGCACGCTGGACAGCCAGGGGAAGCTCACCATGATCCTGGAGGAG
CTGTGGGAGATCAAGGACACCCAGGCACAGCTGGCTGAGGACATCGAGGTGCTGAAGGTGCAGTTTAAGAGAGAATATGG
TTTTATTTCTCAGACCCTGCAAGAAGAGAGATACAGGTACAAGTGACTGGAAGACCAGCTCCATGACATGACGGACCTGC
ATCAGCACGAGACAGCCAACCTGAAACAGGAGCTGGCCAGCATCGAGGACAAGGTGGCCTACCAGGCCTAGGAGCGCTCG
CGGGACATCCAGGGAGCCTTGGAGTCCTGCCAGACTCGCATCTCGAAGCTGGAGCTGCACCAGCAGGAGCAGCAGACGGA
CACCGTGAATGCCAAAGTTCTCCTGGCAAGTGCATCAACATGGTCCTGGCCTTCATGACTGTGATCTTGGTGTGTGTGTC
TACCATCACCAAGTTCGTCTCGCCCATGATGAAGAGCCGCTTCCACATTGTCGGCACCTTCTTTGCTGTGACTCTTCTTG
CAATATTTTGTAAAAACTGGGACCATATTCTGTGTGCCATAGAAAGGATAATAATACCAAGA

Alignment

ORF - retro_ecab_563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VERHDMNTLSLPLNIRRGGSDTNLNFDVPDGILDFHKVKLSADSLKQKILKVTEQIKIEQTSRDGNVAEY
          VERHDMNTLSLPLNIRRGGSDTNLNFDVPDGILDFHKVKLSADSLKQKILKVTEQIKIEQTSRDGNVAEY
Retrocopy VERHDMNTLSLPLNIRRGGSDTNLNFDVPDGILDFHKVKLSADSLKQKILKVTEQIKIEQTSRDGNVAEY

Parental  LKLVSSADKQQASRIKQVFEKKNQKSAHSIAQLQKKLEQYHRKLKEIEQNGASKSSKDFSKDHLKDIQHS
          LKLVSSADKQQA.RIKQVFEKKNQKSAHSIAQLQKKLE.YHRKLKEIEQNGASKSSKDFSKDHL.DIQHS
Retrocopy LKLVSSADKQQAGRIKQVFEKKNQKSAHSIAQLQKKLEKYHRKLKEIEQNGASKSSKDFSKDHLEDIQHS

Parental  LKDAQAKSRTAPGNMESSKSGMPGVSLTPPVFVFSKSREFANLIRNKFGSADNIAHLKNSLEEFRPEASA
          LKDA.AKSRTAPGNMES.KSGMPGVSLTPPVFVF.KSREFANLIRNKFGSADNIAHLKNSLEEFRP.ASA
Retrocopy LKDAHAKSRTAPGNMESGKSGMPGVSLTPPVFVFNKSREFANLIRNKFGSADNIAHLKNSLEEFRPKASA

Parental  RVYGGSATIVNKPKYGSDDECSSGTSGSADSNGNQSFG-AGGAGTLDSQGKLTMILEELREIKDTQAQLA
          RVYG.SATIVNKPKYGSDDECSSGTSGS.DSNGNQS.G.AGGA.TLDSQGKLTMILEEL.EIKDTQAQLA
Retrocopy RVYGDSATIVNKPKYGSDDECSSGTSGSTDSNGNQSSG<AGGASTLDSQGKLTMILEELWEIKDTQAQLA

Parental  EDIEALKVQFKREYGFISQTLQEERYRYERLEDQLHDMTDLHQHETANLKQELASIEEKVAYQAYERSRD
          EDIE.LKVQFKREYGFISQTLQEERYRY..LEDQLHDMTDLHQHETANLKQELASIE.KVAYQA.ERSRD
Retrocopy EDIEVLKVQFKREYGFISQTLQEERYRYK*LEDQLHDMTDLHQHETANLKQELASIEDKVAYQA*ERSRD

Parental  IQEALESCQTRISKLELHQQEQQVLQTDTVNAKVLL-GKCINVVLAFMTVILVCVSTIAKFVSPMMKSRF
          IQ.ALESCQTRISKLELHQQEQQ...TDTVNAKVLL.GKCIN.VLAFMTVILVCVSTI.KFVSPMMKSRF
Retrocopy IQGALESCQTRISKLELHQQEQQ---TDTVNAKVLL<GKCINMVLAFMTVILVCVSTITKFVSPMMKSRF

Parental  HIVGTFFAVTLLAIFCKNWDHILCAIERIIIPR
          HIVGTFFAVTLLAIFCKNWDHILCAIERIIIPR
Retrocopy HIVGTFFAVTLLAIFCKNWDHILCAIERIIIPR

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	0.53 RPM
SRP021940_cerebellum	0.00 RPM	10.39 RPM
SRP021940_embryo	0.03 RPM	5.45 RPM
SRP021940_placental_villous	0.10 RPM	34.21 RPM
SRP021940_synovial_membrane	0.05 RPM	4.23 RPM
SRP021940_testis	0.19 RPM	48.41 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_563 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_563 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011697	1 retrocopy	retro_ecab_563 ,