RetrogeneDB ID: retro_sscr_479

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:138071593..138073165(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016224
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GK
• Ensembl ID: ENSSSCG00000012202
• Aliases: None
• Description: glycerol kinase [Source:HGNC Symbol;Acc:4289]

Sequence

>retro_sscr_479
ATGGCAGCCTCGAAGAAAGCTGTTTTGGGGCCGTTGGTGGGAGCAGTGGACCAGGGCACCAGCTCGACGCGCTTTTTGGT
TTTCAATTCAAAAACAGCCGAACTACTTAGTCATCATCAAGTGGAAATAGAACAAAAATTTCCAAAAGAAGGGTGGGTGG
AACAAGACCCTAAGGAAATCCTGCAGTCCGTCTATGAGTGTATAGAGAAAACGTGTGAGAAACTTGGTCAGCTCAATATT
GATATTTCCAACATAAAAGCTATTGGTGTCAGTAACCAGAGGGAAACCACTGTGGTCTGGGACAAGTTAACTGGAGAACC
CCTCTACAATGCTGTGGTGTGGCTTGATCTAAGAACCCAGTCTACCGTTGCGAACCTTAGTAAAATCATTCCAGTGAATA
ATAACTTTGTCAAGACCAAGACAGGCCTTCCACTCAGCACGTACTTCAGTGCAGTGAAGCTTCGTTGGCTCCTTGATAAT
GTGAGAAAAATTCAAAAGGCAGTTGAAGAAGATAGAGCTCTTTTTGGGACCATTGATTCCTGGCTTATTTGGAGCTTGAC
AGGAGGAGCCAGGGGAGGTGTTCATTGTACAGACGTAACAAATGCAAGTAGGACGATGCTATTCAACATTCATTCTTTGG
AATGGGATAAAGAGCTCTGTGAATTTTTTGAAGTTCCAATGAAAATTCTGCCAAACGTCCGGAGTTCTTCTGAGATCTAT
GGCCTAATGAAAGCTGGGGCCTTGGAAGGCGTGCCAATATCTGGGTGTTTGGGAGACCAGTCTGCTGCATTGGTGGGACA
GATGTGCTTCCAGGATGGACAGGCCAAAAACACGTATGGAACAGGCTGTTTCTTACTATGTAATACAGGCCACAAGTGTG
TGTTTTCTGAACATGGCCTTCTGACCACAGTGGCTTACAAACTTGGCAGAGACAAACCAGTGTATTATGCATTAGAAGGC
TCAGTAGCTATAGCTGGTGCTGTTGTTCGCTGGCTAAGAGACAATCTTGGAATTATAAAGACCTCAGAGGAAATTGAAAA
ACTTGCTAAAGAAGTAGGTACTTCTTATGGCTGTTATTTTGTCCCAGCCTTTTCAGGGCTATATGCACCTTACTGGGAGC
CCAGTGCAAGAGGGATCATCTGTGGGCTCACTCAATTCACCAATAAATGCCATATTGCTTTTGCTGCGTTAGAAGCTGTT
TGTTTCCAAACCCGAGAGATTTTGGATGCCATGAACCGTGACTGTGGAATTCCACTCAGCCATTTGCAGGTAGATGGGGG
AATGACCAACAACAAAATTCTTATGCAGCTACAAGCAGACATTCTGTATATCCCAGTAGTGAAGCCCTCAATGCCAGAAA
CAACCGCCTTGGGAGCTGCCATGGCAGCAGGGGCTGCAGAAGGAGTTGGCGTTTGGAGTCTCAAACCTGAGGATTTATCA
GCTGTCACGATGGAGCGGTTTGAACCTCAGATCAATGCTAAAGAAAGTGAAATTCGTTATTCCACATGGAAGAAAGCTGT
GAAGAAGTCCATGGGTTGGGTTACAACTCAGTATCCAGAAAATGGTGACCCT

Alignment

ORF - retro_sscr_479 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAANKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVELKQEFPKEGWVEQDPKEILNSVYECIEK
          MAA..KAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVE..Q.FPKEGWVEQDPKEIL.SVYECIEK
Retrocopy MAASKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIEQKFPKEGWVEQDPKEILQSVYECIEK

Parental  TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
          TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTV.NLSK.IP.NNNFVK.K
Retrocopy TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVANLSKIIPVNNNFVKTK

Parental  TGLPLSTYFSAVKLRWLLDNVRKVQKAVEEERALFGTVDSWLIWCLTGGANGGVHCTDVTNASRTMLFNI
          TGLPLSTYFSAVKLRWLLDNVRK.QKAVEE.RALFGT.DSWLIW.LTGGA.GGVHCTDVTNASRTMLFNI
Retrocopy TGLPLSTYFSAVKLRWLLDNVRKIQKAVEEDRALFGTIDSWLIWSLTGGARGGVHCTDVTNASRTMLFNI

Parental  HSLEWDKELCEFFEIPMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
          HSLEWDKELCEFFE.PMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
Retrocopy HSLEWDKELCEFFEVPMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG

Parental  TGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIKTSEEIEKLAK
          TGCFLLCNTG.KCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIKTSEEIEKLAK
Retrocopy TGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIKTSEEIEKLAK

Parental  EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNRCHIAFAALEAVCFQTREILDAMNRDCGMPLR
          EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTN.CHIAFAALEAVCFQTREILDAMNRDCG.PL.
Retrocopy EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS

Parental  HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLDPEDLSAVTVERFEPQ
          HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSL.PEDLSAVT.ERFEPQ
Retrocopy HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLKPEDLSAVTMERFEPQ

Parental  INAEESEIRYSTWKKAVMKSMGWVTTQSSESGMP
          INA.ESEIRYSTWKKAV.KSMGWVTTQ..E.G.P
Retrocopy INAKESEIRYSTWKKAVKKSMGWVTTQYPENGDP

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
SRP014902_placenta	0.00 RPM	4.25 RPM
SRP014902_testis	0.00 RPM	2.55 RPM
SRP018288_heart	0.00 RPM	30.04 RPM
SRP018288_kidney	0.10 RPM	184.80 RPM
SRP018288_liver	0.16 RPM	110.82 RPM
SRP018288_lung	0.20 RPM	20.67 RPM
SRP018856_adipose	0.00 RPM	22.26 RPM
SRP035408_brain	0.32 RPM	4.83 RPM
SRP035408_liver	0.00 RPM	94.14 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_sscr_479 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CV871274	138071607	138072264	100	657	0	657
CV875376	138071584	138072214	99.6	627	3	624
CX063319	138071595	138072190	99	589	6	583

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_479 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Pteropus vampyrus	ENSPVAG00000012460	1 retrocopy	retro_pvam_1417,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,
Sus scrofa	ENSSSCG00000012202	2 retrocopies	retro_sscr_479 , retro_sscr_59,