RetrogeneDB ID: retro_ecab_9

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:57158137..57159799(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002394
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GK
• Ensembl ID: ENSECAG00000003599
• Aliases: None
• Description: glycerol kinase [Source:HGNC Symbol;Acc:4289]

Sequence

>retro_ecab_9
ATGGCAGCCCCAAAGAAAGCAGTTGTGGGGCCGTTGGTGGGGGCAGTGGTCCAGGGGACTAACTCTTCTCGCTTTCTGGT
CTTCAATTCAAAAACAGCGGAACTACTTTGTCGCCATCAAGTGGAATTAACACAAGAGTTCCCAAAGGAAGGATGGGTGG
AACAAGACCCTAAGGAAATTCTTCAGTCTGTATATGAGTGTATAGAGAAAACGTGTGAGAAACTTGGCGAGCTGAATATT
AATATATCCAACATAAAAGCTATTGGTGTCAGCAATCAGAGGGAAACCACTGTAATCTGGGACAAGGTAACTGGAGAGCC
GCTCTACAATGCTGTGGTCTGGCTTGATCTAAGAACCCAGTCTACCGTTGAGAATCTTAGTAAAAAAATTCCTGGAAATA
ATAACTTTGTCAAGTCCAAGACGGGCCTTCCACTTAGCACTTACTTCAGTGCAGTAAAACTTCGTTGGATTCTTGACAAC
GTGAGAAAAGTTCAAAAGGCTGTTGAAGAAGGGAGAGCTCTTTTTGGTACCGTTGATTCATGGCTTATCTGGAGTTTGAC
AGGAGGAGTTAATGGAGGCGTCCATTGTACAGATGTAACAAATGCAAGTAGAACAATGCTTTTCAACATCCATTCTTTGG
AGTGGGATAAAGAGCTCTGTGACTTTTTTGAAATTCCAAAGGATATTCTTCCGAAAGTCTGGAGTTCTTCTGAGATCTAT
GGCCTCATGAAAGCTGGGGCTTTGGAAGGTGTGCCAATATCTGGGTGTTTGGGGGACCAGTCGGCTGCATTAGTAGGACA
AATGTGCTTCCAGGAAGGACAAGCCAAAAACACGTATGGAACAGGTTGTTTCTTACTATGTAATACAGGTCGTAAGTGCG
TATTTTCTGAACATGGCCTTCTGACCACAGTGGCTTACAAACTAGGCAGAGATAAGCCAGTATGTTACGCATTGGAAGGT
TCTGTTGCTATAGCAGGTGCTGTTGTTCGCTGGCTAAGAGACAATCTTGGAATTATAGAGACCGCAGAAGAAATTGAAAA
ACTTGCTAAAGAAGTAGGTACTTCTTATGGCTGCTACTTCATCCCAGCTTTTTCAGGGTTATATGCACCTTATTGGGATC
CCAGTGCAAGAGGGCTAATCTGTGGTCTCACTCAGTTTACCAACAAACGTCATATTGCTTTTGCCGCATTAGAAGCTGTT
TGTTTCCAAACCCGAGAGATTTTGGATGCCATGAACCGTGACTGTGGAATTCCACTCAGTCACTTGCAGGTGGATGGAGG
ACTGACCAACAACAAAGTTCTTATGCAACTACAAGCAGACATTCTGCATATTCCAGTAATAAAGTCCTGTATGTCTGAAA
CAACTGCACTGGGAGCTGCCATGGCAGCAGGAGCTGCAGAAGGAGTGGGCGTTTGGAGTCTTGAACCCGAAGATTTGTCA
ACCATCACGATAGAACGGTTTGAACCACGGATCCAAGCCACAGAAAGTAATACTCGTTATTCTACATGGAAGAAAGCTGT
GATGAAGTCAATGGGTTGGGCTACAACTCAGTCTCCTGAAAATGGTGATGCTAATATTTTCTCTAGTCTGCCCTTGGGCT
TTTTTGTAGTGAGTAGCATGATAATGTTAATTGGAGCAAGATACATCTCAGGTGTACCATAA

Alignment

ORF - retro_ecab_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAATKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
          MAA.KKAV.GPLVGAV.QGT.S.RFLVFNSKTAELL..HQVE..QEFP.EGWVEQDPKEILQSVYECIEK
Retrocopy MAAPKKAVVGPLVGAVVQGTNSSRFLVFNSKTAELLCRHQVELTQEFPKEGWVEQDPKEILQSVYECIEK

Parental  TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
          TCEKLG.LNI.ISNIKAIGVSNQRETTV.WDK.TGEPLYNAVVWLDLRTQSTVENLSK.IPGNNNFVKSK
Retrocopy TCEKLGELNINISNIKAIGVSNQRETTVIWDKVTGEPLYNAVVWLDLRTQSTVENLSKKIPGNNNFVKSK

Parental  TGLPLSTYFSAVKLRWLLDNVRKVQKAVEEDRALFGTIDSWLIWSLTGGANGGVHCTDVTNASRTMLFNI
          TGLPLSTYFSAVKLRW.LDNVRKVQKAVEE.RALFGT.DSWLIWSLTGG.NGGVHCTDVTNASRTMLFNI
Retrocopy TGLPLSTYFSAVKLRWILDNVRKVQKAVEEGRALFGTVDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI

Parental  HSLEWDKELCEFFEIPMKVLPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
          HSLEWDKELC.FFEIP...LP.V.SSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQ.GQAKNTYG
Retrocopy HSLEWDKELCDFFEIPKDILPKVWSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQEGQAKNTYG

Parental  TGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIQTSEEIEKLAK
          TGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPV.YALEGSVAIAGAV.RWLRDNLGII.T.EEIEKLAK
Retrocopy TGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVCYALEGSVAIAGAVVRWLRDNLGIIETAEEIEKLAK

Parental  EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
          EVGTSYGCYF.PAFSGLYAPYW.PSARG.ICGLTQFTNK.HIAFAALEAVCFQTREILDAMNRDCGIPLS
Retrocopy EVGTSYGCYFIPAFSGLYAPYWDPSARGLICGLTQFTNKRHIAFAALEAVCFQTREILDAMNRDCGIPLS

Parental  HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
          HLQVDGG.TNNK.LMQLQADIL.IPV.K..M.ETTALGAAMAAGAAEGVGVWSLEPEDLS..T.ERFEP.
Retrocopy HLQVDGGLTNNKVLMQLQADILHIPVIKSCMSETTALGAAMAAGAAEGVGVWSLEPEDLSTITIERFEPR

Parental  INAEESEIRYSTWKKAVMKSMGWVTTQSSESGDPSIFCSLPLGFFIVSSMVMLIGARYISG
          I.A.ES..RYSTWKKAVMKSMGW.TTQS.E.GD..IF.SLPLGFF.VSSM.MLIGARYISG
Retrocopy IQATESNTRYSTWKKAVMKSMGWATTQSPENGDANIFSSLPLGFFVVSSMIMLIGARYISG

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	1.83 RPM
SRP021940_cerebellum	0.00 RPM	7.53 RPM
SRP021940_embryo	0.00 RPM	13.12 RPM
SRP021940_placental_villous	0.87 RPM	10.15 RPM
SRP021940_synovial_membrane	0.00 RPM	10.13 RPM
SRP021940_testis	237.68 RPM	6.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_9 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_9 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_9 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_2

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009161	1 retrocopy	retro_amel_45,
Canis familiaris	ENSCAFG00000013713	1 retrocopy	retro_cfam_19,
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Equus caballus	ENSECAG00000003599	1 retrocopy	retro_ecab_9 ,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Myotis lucifugus	ENSMLUG00000001046	2 retrocopies	retro_mluc_151, retro_mluc_853,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,