RetrogeneDB ID: retro_ggor_3018

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:58310484..58312474(-)
• Located in intron of: ENSGGOG00000025619

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD1
• Ensembl ID: ENSGGOG00000005251
• Aliases: None
• Description: None

Sequence

>retro_ggor_3018
CCCGTTCCTGGTGGCTTAGGGCTCATGACGGTTGCAATGCTCATGCAGAGCACTGTAGAGAGTGCCAAGCGTTTCCTGGA
GAAATTTAAGCCAGGAAAGTGGATGATTCAGTATAACAACCTTAACCTCAAGACACCTGTTCCAAGTGACATTGATATAT
CATGATCTTGTAAACCGAAGCCCATTGGTAAGCTGGCTTGAGGAATTGGTCTGCTGTCTGAAGAGGTAGAATTATATGGT
GAAACAAAGGCCAAAGTTCTGCTGTCAGCACTAGAATGCCTGAAGCACCAGCCTGATGGGAAATATCAGGTGGTGACTGG
AATAACTCCAACACCCCTGGGAGAAGGGAAAAGCACGACTACAATCGGGCTGGTGCAAGCCCTTCTTGCCCATCTCTACC
AGAACTTTTTTATGTGTGTGCGACAGCCTTCTCAGGGCCCCACCTTTGGAATAAAAGGTGGTGCTGCAGGAGGCGGCTAC
TCCCAGGTCATTCCTATGGAAGAGTTTAATCTCCACCTCACAGGTGACATCCATGCCATCACTGTATCTAATAACCTTGT
TGCTGCGGCTATTGATGCTCAGATATTTCATGAACTGACCCAGACAGACAAGGCTATCTTTACTCATTTGGTGCCATCAG
TAAATGGAGTGAGAAAGTTCTCTGATATCCACATACAAAGGTTAAACAGACTAGGCATTGACAAGACTGACTCTACCACA
CTGATAGATGAAGAGATAAACAGATTTGCAAGATTGGACATTGATCCAGAAACCACAGCTTGGCAAAGAGTGTTGAATAC
CAATGATAGATTCCTGAGGAAGATCACGATTGGACAGGCTCCAACGAAGAAAAGTCACACACAGACGGTCCACTTTGATA
TCTCTGTGGCCAGTGAAATTATGGCTGTCCTGGCTCTCACCACTTCTCTAGAAGACAGGAGAGAGAGACTGGGAAAAATG
GTGGTGGCATCCAGTAAGAAAGGAGAGCCCGTCAGTGCTGAAGATCTGGGGATGAGTGGTGCATTGATAGTGCTTATGAA
GGACACAAGCAAGCCCAATCTCATGCAGAGATTGGAGGGCACTCCAGTGTTTGTCCATGCCGGCCCATTTGCCAACATCG
CACACGGCAATTCCTCTATCATTGAAGACCGGATCACACTCTAGCTTGTTGGCCCAGAAGGGTTTGTAGTGACGGAGGCG
GGATTTGGAGCAGACATTGGGATAGAAAAATTTTTTAACATCAAATCCCAGTATTCCGGTCTCCACCCTCACGTGGTGGT
GCTTGTTGCCACTGTCAGCGCTCTAAAGATGCACAGGGGTGGCCCTATGGTCACTGCTGGAATGCCTCTTCCCAAGGCTT
ACATAGAGGAGAACCTGGAGCTGGTTGAAAAAGGCTTCAGTAACTTGAAGAAACAAACTGAAAATGCCGGAATGTTTGGA
ATTCCAATAGTAGTGGCCGTGAATGCATTCAAGACAGATACAGAGACTGAGCTGGACCTCATCGGCTGCCTTTCCAGAGA
ACAGAGGGCTTTTGATGCCGTGAAGTGCACTCACTGGCAGAAGGGGGCAAGGGTACCTTAGCCCTGGCTCAGGCTGTCCA
GAGAGCAGGACAAGCACCCAGCAGCTTCCAACTCCTTTATGACCTCAAGCTCCCAGTTGAGGATAAAATCAGGATCATTG
CACAGAAGATCTATGGAGCAGACAACATTGAATTACTCCTCAAAGTTCAACACAAAGCTGAAGTCTACACAAAGCAGGGC
TTTGGGAATCTCCCCATCTGCATGGCCAAAACACACTTGTCCTTGTCTCACAACGCAGAACGAAAAGGTGTCCCTACAGG
ATTCGTTCTGACCATTCGTGACATCCATGCCAGCATCGGGGCTGGTTTTCTGTACCCTTTAGTAGGAACGATGAGCACAA
TGGACTCCCCACCCAGCCCTGTTTTTATGATACTGATTTGGACCCTGAAACAGAACAGGTGAATGGATTA

Alignment

ORF - retro_ggor_3018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 71.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVPGGVGPMTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNFKTPVPSDIDISRSCKPKPIGKLAREIG
          PVPGG.G.MTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLN.KTPVPSDIDIS.SCKPKPIGKLA..IG
Retrocopy PVPGGLGLMTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNLKTPVPSDIDIS*SCKPKPIGKLA*GIG

Parental  LLSEEVELYGETKAKVLLSALERLKHRPDGKYVVVTGITPTPLGEGKSTTTIGLVQALGAHLYQNVFACV
          LLSEEVELYGETKAKVLLSALE.LKH.PDGKY.VVTGITPTPLGEGKSTTTIGLVQAL.AHLYQN.F.CV
Retrocopy LLSEEVELYGETKAKVLLSALECLKHQPDGKYQVVTGITPTPLGEGKSTTTIGLVQALLAHLYQNFFMCV

Parental  RQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDARIFHELTQTDKALFNRL
          RQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAIT..NNLVAAAIDA.IFHELTQTDKA.F..L
Retrocopy RQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITVSNNLVAAAIDAQIFHELTQTDKAIFTHL

Parental  VPSVNGVRRFSDIQIRRLKRLGIEKTDPTTLTDEEINRFARLDIDPETITWQRVLDTNDRFLRKITIGQA
          VPSVNGVR.FSDI.I.RL.RLGI.KTD.TTL.DEEINRFARLDIDPET..WQRVL.TNDRFLRKITIGQA
Retrocopy VPSVNGVRKFSDIHIQRLNRLGIDKTDSTTLIDEEINRFARLDIDPETTAWQRVLNTNDRFLRKITIGQA

Parental  PTEKGHTRTAQFDISVASEIMAVLALTTSLEDMRERLGKMVVASSKKGEPVSAEDLGVSGALTVLMKDAI
          PT.K.HT.T..FDISVASEIMAVLALTTSLED.RERLGKMVVASSKKGEPVSAEDLG.SGAL.VLMKD..
Retrocopy PTKKSHTQTVHFDISVASEIMAVLALTTSLEDRRERLGKMVVASSKKGEPVSAEDLGMSGALIVLMKDTS

Parental  KPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADRIALKLVGPEGFVVTEAGFGADIGMEKFFNIKCRYSG
          KPNLMQ.LEGTPVFVHAGPFANIAHGNSSII.DRI.L.LVGPEGFVVTEAGFGADIG.EKFFNIK..YSG
Retrocopy KPNLMQRLEGTPVFVHAGPFANIAHGNSSIIEDRITL*LVGPEGFVVTEAGFGADIGIEKFFNIKSQYSG

Parental  LCPHVVVLVATVRALKMHGGGPTVTAGLPLPKAYIQENLELVEKGFSNLKKQIENARMFGIPVVVAVNAF
          L.PHVVVLVATV.ALKMH.GGP.VTAG.PLPKAYI.ENLELVEKGFSNLKKQ.ENA.MFGIP.VVAVNAF
Retrocopy LHPHVVVLVATVSALKMHRGGPMVTAGMPLPKAYIEENLELVEKGFSNLKKQTENAGMFGIPIVVAVNAF

Parental  KTDTESELDLISRLSREHGAFDAVKCTHW-AEGGKGALALAQAVQRAAQAPSSFQLLYDLK--VGDLLSA
          KTDTE.ELDLI..LSRE..AFDAVKCTHW.AEGGKG.LALAQAVQRA.QAPSSFQLLYDLK..V.D....
Retrocopy KTDTETELDLIGCLSREQRAFDAVKCTHW<AEGGKGTLALAQAVQRAGQAPSSFQLLYDLKLPVEDKIRI

Parental  KKEKXXXADDIELLPEAQHKAEVYTKQGFGNLPICMAKTHLSLSHNPEQKGVPTGFVLPIRDIRASVGAG
          ...K...AD.IELL...QHKAEVYTKQGFGNLPICMAKTHLSLSHN.E.KGVPTGFVL.IRDI.AS.GAG
Retrocopy IAQKIYGADNIELLLKVQHKAEVYTKQGFGNLPICMAKTHLSLSHNAERKGVPTGFVLTIRDIHASIGAG

Parental  FLYPLVGTMSTMPGLPTRPCF-YDIDLDPETEQVNGL
          FLYPLVGTMSTM...P..P.F.YD.DLDPETEQVNGL
Retrocopy FLYPLVGTMSTMDS-PPSPVF<YDTDLDPETEQVNGL

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
SRP007412_brain_prefrontal_cortex	1.05 RPM	36.88 RPM
SRP007412_cerebellum	0.55 RPM	25.81 RPM
SRP007412_heart	0.59 RPM	23.05 RPM
SRP007412_kidney	5.52 RPM	140.41 RPM
SRP007412_liver	6.88 RPM	168.37 RPM
SRP007412_testis	0.41 RPM	21.55 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_3018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3018 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4839
Pan troglodytes	retro_ptro_3223

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015967	1 retrocopy	retro_cfam_300,
Homo sapiens	ENSG00000100714	1 retrocopy	retro_hsap_4839,
Gorilla gorilla	ENSGGOG00000005251	1 retrocopy	retro_ggor_3018 ,
Microcebus murinus	ENSMICG00000013011	6 retrocopies	retro_mmur_1069, retro_mmur_1250, retro_mmur_1462, retro_mmur_451, retro_mmur_777, retro_mmur_993,
Macaca mulatta	ENSMMUG00000001319	1 retrocopy	retro_mmul_2583,
Pan troglodytes	ENSPTRG00000006435	1 retrocopy	retro_ptro_3223,