RetrogeneDB ID: retro_ecab_47

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:53653367..53655314(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000005116
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000011807
• Aliases: None
• Description: None

Sequence

>retro_ecab_47
ATGGAGCACATACAGGGGGCCTGGAAGACGATCAGCAGTGGTTTTGGATTCAAAGACGCGGTGTTTGATGGCCCCAGCTG
TATCTGCCCTACAATAGTTCAGCAGTTTGGCTATCAGCGTCGGGCGTCAGATGATGGCAAACTTACGGACTCTTCTAAGA
CAAGCAACACTATCTGTGTTTTCTTGCCAAATAAGCAAAGAACGGTGGTCAGTGTGCGAAATGGAGTGAGCTTGCATGAC
TGCCTTATGAAAGCACTCAAGGTGAGGGGCCTGCAACCGGAGTGCTGTGCAGTGTTCAGACTTCTCCACGAACACAAAGG
TAAAAAAGCACGTTTAGATTGGAATACTGATGCTGCCTCATTGATTGGAGAAGAACTTCAAGTAGATTTCCTGGATCATG
TTCCTCTCACAACACACAGCTTTGCTCGGAAGACCTTTCTGAAGCTTGCCTCTTGTGACATCTGTCAGAAGTTCTTGCTA
AATGGATTTCGATGTCAGACTTGTGGCTACAAATTTCATGAGCACTGTAGCACCAAAGTACCTACGATGTGTGTGGACTG
GAGTAATATCAGACAACTCTTATTGTTTCCAAATTCCACTTTTGGTGATAGTGGAGTCCCAGCACTGCCTTCCTTGACAA
TGCGTCGGATGCGAGAGTCTGTTTCCCGGATGCCTGTTAGTTCCCAGCACAGATACTCCACGCTCCACGCCTTCACACTC
AACATCTCCAGTTCCTGCTCTGAAGGTTCCCTCTCCCAGAGGCAGAGGTCAACGTCCACACCTAATGTCCACATGGTCAG
CACCACCCTGCCTGTGGACAGCAGGGTGATTGAGGATGCAATTCGAAGTCACAGTGAATCAGCTTCACCTTCAGCCTTGT
CTAGCAGCCCCAACAATCTGAGCCCAACGGGCTGGTCACAGCCTAAAACCCCTGTGCCAGCACAGAGAGAGCGGGCACCA
GGATCCGGGACCCAGGAGAAAAACAAAATTAGACCTCGTGGTCAGAGAGATTCAAGCTGTTACTGGGAAATAGAAGCCAG
TGAAGTGATGCTCTCCACTCGGATTGGGTCAGGCTCCTTTGGAACTGTGTATAAGGGCAAATGGCACGGAGACGTTGCAG
TGAAAATCTTAAAGGTTGTTGACCCCACATCAGAGCACTTCCAGGCATTCAGGAACAAGGTGGCTGTCCTGCATAAAACA
CGGCACGTGAACGTCCTGCTCTTCATGGGGTACATGACGAAGGATAACCTGGCAATTGTGACCCAGTGGTGTGAGGGCAG
CAGCCTCTACAAACACTTGCATGTCCAGGAGACCAAGTTCCAGATGTTCCAGTTGATTGACATCACCCGGCAGACAGCTC
AGGGAATGGACTATTTGCATGCAAAAAACATCATCCACAGAGATATGAAGTCCAAAAATATATTTCTCCACGAAGGCCTG
ACGGTGAAAATTGGAGACTTTGGTTTGGCAACAGTCAAGTCGCGCTGGAGTGGTTCTCAGCAGGTTGAACAACCCACTGG
CTCTGTCCTGTGGTTGGCCCCAGAGGTGATCCGAATGCAGGATAATAACCCGTTCAGCTTCCAGTCCGATGTCTACTCCT
ATGGCATTGTACTGTATGAGCTCATGACAGGGGAACTGCCTTACTCCCACATCAACAACCGAGATCAGATCCTCTTCATG
GTGGGCCGAGGATATGCCTCCCCAGACCTTAGTAAGCTATACAAGAACTGCCCCAAAGCAGTGAAGAGGCTTGTGGCTGA
CTGCGTGAAGAAAGTTAAGGAGGAGAGGCCTCTTTTTCCCCAGATCTTGTCTCCCGTTGAGTTGCTCCAACACTCTCTAC
CGAAAATCAACCGGAGTGCTTCTGAGCCATCCCTGCATCGGGCGGCCCACACCAAGGACATCAATGCCTGCACGTTGACC
ACGTCCCCTAGACTACCTGTCTTCTAG

Alignment

ORF - retro_ecab_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.07 %
• Parental protein coverage: 55.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSSSPNNLSPTGWSQPKTPVPAQRERAPGSGTQEKNKIRPRGQRDSSYYWEIEASEVMLSTRIGSGSFGT
          LSSSPNNLSPTGWSQPKTPVPAQRERAPGSGTQEKNKIRPRGQRDSS.YWEIEASEVMLSTRIGSGSFGT
Retrocopy LSSSPNNLSPTGWSQPKTPVPAQRERAPGSGTQEKNKIRPRGQRDSSCYWEIEASEVMLSTRIGSGSFGT

Parental  VYKGKWHGDVAVKILKVVDPTPEQFQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKH
          VYKGKWHGDVAVKILKVVDPT.E.FQAFRN.VAVL.KTRHVN.LLFMGYMTKDNLAIVTQWCEGSSLYKH
Retrocopy VYKGKWHGDVAVKILKVVDPTSEHFQAFRNKVAVLHKTRHVNVLLFMGYMTKDNLAIVTQWCEGSSLYKH

Parental  LHVQETKFQMFQLIDIARQTAQGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQV
          LHVQETKFQMFQLIDI.RQTAQGMDYLHAKNIIHRDMKS.NIFLHEGLTVKIGDFGLATVKSRWSGSQQV
Retrocopy LHVQETKFQMFQLIDITRQTAQGMDYLHAKNIIHRDMKSKNIFLHEGLTVKIGDFGLATVKSRWSGSQQV

Parental  EQPTGSVLWMAPEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQIIFMVGRGYASPDLSK
          EQPTGSVLW.APEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQI.FMVGRGYASPDLSK
Retrocopy EQPTGSVLWLAPEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQILFMVGRGYASPDLSK

Parental  LYKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRSASEPSLHRAAHTEDINACTLTTS
          LYKNCPKA.KRLVADCVKKVKEERPLFPQILS..ELLQHSLPKINRSASEPSLHRAAHT.DINACTLTTS
Retrocopy LYKNCPKAVKRLVADCVKKVKEERPLFPQILSPVELLQHSLPKINRSASEPSLHRAAHTKDINACTLTTS

Parental  PRLPVF
          PRLPVF
Retrocopy PRLPVF

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	0.35 RPM	25.97 RPM
SRP021940_cerebellum	0.10 RPM	21.50 RPM
SRP021940_embryo	0.87 RPM	46.62 RPM
SRP021940_placental_villous	0.38 RPM	26.03 RPM
SRP021940_synovial_membrane	0.77 RPM	31.13 RPM
SRP021940_testis	0.58 RPM	22.64 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_47 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_47 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_47 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011807	1 retrocopy	retro_ecab_47 ,
Macaca mulatta	ENSMMUG00000007450	1 retrocopy	retro_mmul_2506,
Tarsius syrichta	ENSTSYG00000007438	1 retrocopy	retro_tsyr_1876,