RetrogeneDB ID: retro_ecab_439

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:974344..975240(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCBP
• Ensembl ID: ENSECAG00000015053
• Aliases: None
• Description: syndecan binding protein (syntenin) [Source:RefSeq peptide;Acc:NP_001229406]

Sequence

>retro_ecab_439
ATGTCTCTGTACCCATCTCTTGAAGACCTGAAGGTAGACAAAGTAATTCAGGCTCAACTGCCTATTCTGCAAACCCTGCC
AACCCAGCAGTTTTGTCTGAAGCTTCTGCTCCTCCCATCTCTCAAGATGGAAATCTCTATCCTAAGCTGTATCCAGAGCT
CTCTCAGTACATGGGCCTGAGTTTAAATGATGAAGAAATACGTGCAAATATGGCCATGGTCCCTGGAGCACCAATTCAGG
GACAATTGGTAGCAAGACCTTCCAGTAAGAACTATATGATGGCTCCTGTAACTGGCAATGATGTTGGGATTCGTAGAGCA
GAAATTAAGCAAGGGATTCGTGAAGTCATCCTGTGTAAGGATCAAGATGGAAAAATTGGGCTCAGGCTTAAAGCAAGAGA
CAACGGAATATTTGTTCAGCTAGCCCAGGCAAATTCTCCAGCCTCGCTGGTTGGCCTGAGGTTTGGGGACCAAGTACTCC
AGATCAACGGGGAAAACTGTGCAGGCTGGAGCTCTGATAAATCGCACAAGGTGCTCAAACAGGATTTTGGAGAGAAGATT
ACTATGACTATTCGTGACAGGCCCTTCGAATGAACAATTACCATGCATAAGGATAGTACTGGACATGTTGGTTTTATCTT
TAAAAATGGAAAAATAACATCCGTAGTGAAAGATAGTTCTGCAGCCAGAAATGGTCTCCTCACAGAACATAACATCTGTG
AGATCAATGGACAGAATGTCATTGGGCTGAAGGACTCTCAAATTGCAGGCATACTGTCAACATCTGAGACTGTGGTTACT
ATTACAATCATGCCTGCTTTTATCTTTGAACATATTATTAAACGGATGGCACCAAGCATTATGAAAAGCCTGATGGATCA
CACCATTCCTGAGATT

Alignment

ORF - retro_ecab_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLYPSLEDLKVDKVIQAQ-TAYSANPANPAVLSEASAPPVSQDGNLYPKLYPELSQYMGLSLNDEEIRA
          MSLYPSLEDLKVDKVIQAQ.TAYSANPANPAVLSEASAPP.SQDGNLYPKLYPELSQYMGLSLNDEEIRA
Retrocopy MSLYPSLEDLKVDKVIQAQ<TAYSANPANPAVLSEASAPPISQDGNLYPKLYPELSQYMGLSLNDEEIRA

Parental  NMAMIPGAPIQGQLVARPSSMNYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGVFV
          NMAM.PGAPIQGQLVARPSS.NYM.APVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLK..DNG.FV
Retrocopy NMAMVPGAPIQGQLVARPSSKNYMMAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKARDNGIFV

Parental  QLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKSHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGH
          QL.QANSPASLVGLRFGDQVLQINGENCAGWSSDKSHKVLKQ.FGEKITMTIRDRPFE.TITMHKDSTGH
Retrocopy QLAQANSPASLVGLRFGDQVLQINGENCAGWSSDKSHKVLKQDFGEKITMTIRDRPFE*TITMHKDSTGH

Parental  VGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIFEHI
          VGFIFKNGKITS.VKDSSAARNGLLTEHNICEINGQNVIGLKDSQIA.ILSTS.TVVTITIMPAFIFEHI
Retrocopy VGFIFKNGKITSVVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIAGILSTSETVVTITIMPAFIFEHI

Parental  IKRMAPSIMKSLMDHTIPEV
          IKRMAPSIMKSLMDHTIPE.
Retrocopy IKRMAPSIMKSLMDHTIPEI

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	0.30 RPM	26.33 RPM
SRP021940_cerebellum	0.21 RPM	19.89 RPM
SRP021940_embryo	0.59 RPM	28.21 RPM
SRP021940_placental_villous	1.59 RPM	66.78 RPM
SRP021940_synovial_membrane	0.91 RPM	59.05 RPM
SRP021940_testis	0.19 RPM	8.18 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_439 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_439 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035, retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439 ,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,