RetrogeneDB ID: retro_ecab_749

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 30:616681..617648(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABI1
• Ensembl ID: ENSECAG00000015467
• Aliases: None
• Description: abl-interactor 1 [Source:HGNC Symbol;Acc:11320]

Sequence

>retro_ecab_749
AAGCATGGAAATAACCAGCCTGCAAGAACTGGCACTCTGTCGAGAACAAATCCTCCTACTCAGAAGCCACCGAGTCCTCC
CACGTCAGGCCGGGGACGCTGGGGCGGAATACTCCTTACAAAACCCTGGAGCCTGTTAAACCCCACCGTTCCTAGTGACT
ACATGACAAGTCCTGCTACGCTCGGAAGTCAGCATAGCCCAGGCAGGACAGCTTCTTTAAATCAGAGACCGAGGACACAC
AGTGGAAGCAGTGGAGGAAGTGGAAGTCGAGAAAACAGTGGAAGCAGCAGTATTGGCATTCCCACTGCCGTGCCTACACC
CTCAGCACCCGCTGTTGGACCAGCCGCCCGCGGCTCAGCTCCTGGTTCCCAGTACGGCACAATGACCAGGCAGATCTCTC
AACACAACTCTACCACTTCCTCGACATCTTCTGCTGCATACAGACGAACTCCGTCTGTGACTGCTCAATTTTCTGCTCAG
CCTCATGTTAATGGAGGTCCACTTTATTCTCAAAATTCAATTTCTATTGCTCCACCCCCTCCCCGTACGCCTCAGTTGAC
TCCACAGATACCTCTCATAGGCTTCGTGGCCTGGGGGCAGGAAAACATTGCTGATAGTCCAACTCCACCCCCACCCACCT
CCACCAGATGACATTCCCATGTTTGATGACTCTTCACCTCCACAGCACCACCTCCAGTGGATTATGAAGACAAGGAGGCT
GCAGTGGTTCAGTATAATGATCCAAATGCAGATGGGGATCCTGCTTGGGCCCGCAAGAATTATATTGAGAAAGTTGTGGC
AATATATGGTTATACAAAAGACAAAGATGATGAGCTATCATTTATGGAGAGTACAATCATTTGTGTAATAAAGAAGAATG
ATGACGACTGGTATGAAGGAGTCTGCAATCAGAGTGACTGGTCTGTTCCCTGGGAACTATGTCACATCAATCATGTACTA
GACTGAT

Alignment

ORF - retro_ecab_749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.67 %
• Parental protein coverage: 72.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KHGNNQPARTGTLSRTNPPTQK---PPSPPMSGRGTLGRNTPYKTLEPVKPPTVPNDYMTSPARLGSQHS
          KHGNNQPARTGTLSRTNPPTQK...PP.......G......P...L.....PTVP.DYMTSPA.LGSQHS
Retrocopy KHGNNQPARTGTLSRTNPPTQKPPSPPTSGRGRWGGILLTKPWSLLN----PTVPSDYMTSPATLGSQHS

Parental  PGRTASLNQRPRTHSGSSGGSGSRENSGSSSIGIPIAVPTPSPPTIGPAAPGSAPGSQYGTMSRQISRHN
          PGRTASLNQRPRTHSGSSGGSGSRENSGSSSIGIP.AVPTPS.P..GPAA.GSAPGSQYGTM.RQIS.HN
Retrocopy PGRTASLNQRPRTHSGSSGGSGSRENSGSSSIGIPTAVPTPSAPAVGPAARGSAPGSQYGTMTRQISQHN

Parental  STTSSTSSGGYRRTPSVTAQFSAQPHVNGGPLYSQNSISIAPPPPPMPQLTPQIPLTGFVARVQENIADS
          STTSSTSS..YRRTPSVTAQFSAQPHVNGGPLYSQNSISIAPPPP..PQLTPQIPL.GFVA..QENIADS
Retrocopy STTSSTSSAAYRRTPSVTAQFSAQPHVNGGPLYSQNSISIAPPPPRTPQLTPQIPLIGFVAWGQENIADS

Parental  PTPPP-PPPPDDIPMFDDSPPP-PPPPPVDYEDEEAAVVQYNDPYADGDPAWAPKNYIEKVVAIYDYTKD
          PTPPP.PPPPDDIPMFDDS.PP...PPPVDYED.EAAVVQYNDP.ADGDPAWA.KNYIEKVVAIY.YTKD
Retrocopy PTPPP>PPPPDDIPMFDDSSPP<TAPPPVDYEDKEAAVVQYNDPNADGDPAWARKNYIEKVVAIYGYTKD

Parental  KDDELSFMEGAIIYVIKKNDDGWYEGVCN-RVTGLFPGNYVESIMHYTD
          KDDELSFME..II.VIKKNDD.WYEGVCN.RVTGLFPGNYV.SIM..TD
Retrocopy KDDELSFMESTIICVIKKNDDDWYEGVCN>RVTGLFPGNYVTSIMY*TD

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	0.12 RPM	42.91 RPM
SRP021940_cerebellum	0.00 RPM	38.07 RPM
SRP021940_embryo	0.43 RPM	29.69 RPM
SRP021940_placental_villous	0.48 RPM	49.36 RPM
SRP021940_synovial_membrane	0.52 RPM	36.73 RPM
SRP021940_testis	0.77 RPM	26.28 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_749 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_749 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	ENSECAG00000015467	1 retrocopy	retro_ecab_749 ,