RetrogeneDB ID: retro_cfam_300

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:29901372..29903047(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD1
• Ensembl ID: ENSCAFG00000015967
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase [Source:HGNC Symbol;Acc:7432]

Sequence

>retro_cfam_300
GGAGCTAGTCAATCATCAATTTTGGTGGTGTCTGTCATGGGCAGCAGACTAATAAAGGTCATGATATCAGCAGAAATCCT
GAACGGGAAGGTGGTCTTTGTGCAAATAAGGGAGAGACTGAAGAACCAAGTCACTCAGATGAAGGAGCAAGTTCTGGTTT
TACACCAGGCCTGGCAATTTTACAGGTTAATGACAGAGATGATTCTAATCTTTATATAAATGTGAAGCTGAAAGCTGCTG
AAGAGATTGGGATCAGAGCACACACATTAAATTACCAAGAACAGCCACAGAATCTGAGGTGTTAAAGTATGTTGCATCAT
TGAATGAAGACCTCACTGTCCATGGTTTCATAGTGCAGCTGCCTTTAGATTCGGAGAACCCCATTAACACTGAAGCAGTG
GTCAATGCTGTTGTACCTGAAAAGGATGTGGATAGGTTGACTAGCATCAGTGCTGGAAAACTTGCTAGAGGTGACCTGAA
TGACTGTTTCATCCATCGTACACCTAAAGGATGCTTGGAACTCATCAAAGAGACAGGGGTATAGGTTGCTGGAAGGCACG
CTGTAGTGGTTGGGCTCAGTAAGATAGTTGGTGCTCTGATGCATGACCTGGTTCTGTGGAACCATGCCACAGTGACCACC
TGCCACTCCAAGACTGCCAAACTAGGCAAGGAGGTAAATAAAGGTGACATCCTGGTGGTAGCAACTGGTCAGCCACAAAT
GGTAAAATGGGAGTGGATCTAACCTGCAATAGTCATCGACTGCAGGATCAATTATATTACAGGTGATACAAAACCAAATG
GGAGAAAAGTGGTAGGTGATGTGGCATACAATGAGGCCAAAGAGAGGGCAGGCTTCATCACTCCTGTTCCTGGTAGCATG
GGGCCCATGATGGCGACAATGCTAATGCAGAGCACAGTGGAGAGCAAAGCGTTTCCTGGAGAAATTTAAGCCAGGAAAGT
GGATGATTCAATATAACAACCTTAACCTCAAGACTCCTGTTCCAAGTGACATTGATATATCATGGTCTTGTAAGCCAAAG
CCCATTGGCAGCCTGGCTCAGGAAATTGGTCTGCTCTCTGAAGAGATGGAATTGTACGGTGATACAAAGGCCAAGGTTCT
GCTGTCAGCACTGGAACGCCTGAAGCACCAGTCTGATGGGAAATACGTGGTGGTGACTGGAATCACCCCCAATGCCCCTG
GGAGAAGGGAAAAGCACAGCCACCATTGGGCTGGTGCAGGCCCTTGGCACCCATCTTCATCAGAACGTCTTTGCGTGTGT
ACGACAGCCTTCTCAGGGCCCCACCTTTGGAATAAAAGATGGCATTGCAAGAGGTGGCTACTCACAGGTCATTCCTATGG
AACAGTTTGATCTCTACCTCACTGGTGACATCCATGCCATCGCTGCAGTGAATAACCTTGTCGCTGCAGCCATCGATGCC
CAGATGTTCCACAAACTGATGCAGACAGACAAGGGTCTCTTTAATCATTTGGTACCATCAGTAAATGGAGTGAGAAAGTT
CTCTGATATCCAAATCCGAAGGTTACAACGACTGAGTATTGAAAAAACTGACCCTACCCCACTGACTGATGACCGAGATA
AACAGATTTGCAAGATTGGACATTGATCCAGAAACCATAACTTGGCAAAGAGTATTGGATACCAATGATAGATTC

Alignment

ORF - retro_cfam_300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 57.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GASRSSVLVVSIVGSGLIKAMAPAEILNGKVVSAQIRERLKNEVTQMKEQV-PGFIPGLAILQVGDRDDS
          GAS.SS.LVVS..GS.LIK.M..AEILNGKVV..QIRERLKN.VTQMKEQV..GF.PGLAILQV.DRDDS
Retrocopy GASQSSILVVSVMGSRLIKVMISAEILNGKVVFVQIRERLKNQVTQMKEQV<SGFTPGLAILQVNDRDDS

Parental  NLYINVKLKAAEEIGIRA-THIKLPKTATESEVLKYVTSLNEDLTVHGFIVQLPLDSENPINTEAVINAI
          NLYINVKLKAAEEIGIRA.THIKLP.TATESEVLKYV.SLNEDLTVHGFIVQLPLDSENPINTEAV.NA.
Retrocopy NLYINVKLKAAEEIGIRA<THIKLPRTATESEVLKYVASLNEDLTVHGFIVQLPLDSENPINTEAVVNAV

Parental  VPEKDVDGLTSISAGKLARGDLKDCFIPCTPKGCLELIKETGVQIAGRHAVVVGRSKIVGAPMHDLLLWN
          VPEKDVD.LTSISAGKLARGDL.DCFI..TPKGCLELIKETGV..AGRHAVVVG.SKIVGA.MHDL.LWN
Retrocopy VPEKDVDRLTSISAGKLARGDLNDCFIHRTPKGCLELIKETGV*VAGRHAVVVGLSKIVGALMHDLVLWN

Parental  HATVTTCHSKTANLSEEVNKGDILVVATGQPEMVKGEWIKPGAIVIDCGINYIPDDTKPNGRKVVGDVAY
          HATVTTCHSKTA.L..EVNKGDILVVATGQP.MVK.EWI.P.AIVIDC.INYI..DTKPNGRKVVGDVAY
Retrocopy HATVTTCHSKTAKLGKEVNKGDILVVATGQPQMVKWEWI*P-AIVIDCRINYITGDTKPNGRKVVGDVAY

Parental  NEAKERAGFITPVPGGVGPMTVAMLMQSTVESAKRF-LEKFKPGKWMIQYNNLNLKTPVPSDIDISRSCK
          NEAKERAGFITPVPG..GPM...MLMQSTVES.K.F.LEKFKPGKWMIQYNNLNLKTPVPSDIDIS.SCK
Retrocopy NEAKERAGFITPVPGSMGPMMATMLMQSTVES-KAF>LEKFKPGKWMIQYNNLNLKTPVPSDIDISWSCK

Parental  PKPIGSLAREIGLLSEEVELYGDTKAKVLLSALERLKHQPDGKYVVVTGITPT-PLGEGKSTTTIGLVQA
          PKPIGSLA.EIGLLSEE.ELYGDTKAKVLLSALERLKHQ.DGKYVVVTGITP..PLGEGKST.TIGLVQA
Retrocopy PKPIGSLAQEIGLLSEEMELYGDTKAKVLLSALERLKHQSDGKYVVVTGITPN>PLGEGKSTATIGLVQA

Parental  LGAHLHQNVFACVRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDARMFH
          LG.HLHQNVFACVRQPSQGPTFGIK.G.A.GGYSQVIPME.F.L.LTGDIHAI.A.NNLVAAAIDA.MFH
Retrocopy LGTHLHQNVFACVRQPSQGPTFGIKDGIARGGYSQVIPMEQFDLYLTGDIHAIAAVNNLVAAAIDAQMFH

Parental  ELTQTDKALFNRLVPSVNGVRKFSDIQIRRLQRLGIEKTDPTTLTDD-EINRFARLDIDPETITWQRVLD
          .L.QTDK.LFN.LVPSVNGVRKFSDIQIRRLQRL.IEKTDPT.LTDD.EINRFARLDIDPETITWQRVLD
Retrocopy KLMQTDKGLFNHLVPSVNGVRKFSDIQIRRLQRLSIEKTDPTPLTDD>EINRFARLDIDPETITWQRVLD

Parental  TNDRF
          TNDRF
Retrocopy TNDRF

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
SRP012049_cerebellum	0.08 RPM	68.75 RPM
SRP017611_brain	0.00 RPM	50.18 RPM
SRP017611_kidney	0.00 RPM	285.68 RPM
SRP017611_liver	0.00 RPM	267.43 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_300 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_300 has 0 orthologous retrocopies within eutheria group .

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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,