RetrogeneDB ID: retro_cfam_1330

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:12220957..12222368(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METAP2
• Ensembl ID: ENSCAFG00000006353
• Aliases: None
• Description: methionyl aminopeptidase 2 [Source:HGNC Symbol;Acc:16672]

Sequence

>retro_cfam_1330
GTGGCAGGCGTGGAGGAGGCAGCGTCCTCTGGGAGCCACCTGAATGGCGACCTGGATCCAAACGACAGAGAAGATGGAGC
TGCCTCTACCACTGAGGAAGCAGCCAAGAAAAAAAGATGGAAGAACAAGAGTAAAGGGGCTGCCACAGCAGGAAAACAAG
AACCTGATAAAGAATCAGGAGCCTCAGTTGATGAGGTAGCAAGACAATTGTAAAGCAAGCATTGGAAGAGAAAGAGAGAG
ATGATGACGATGGAGATGGGGATGGAGATGGAGCAACTGGAAAGAAGAAAAAGAAGAGAGGACCAAAAGTTCAAACAGAC
CCTCCCTCAGTTCCAGTGTGTGACCTGTATCCTAATGGTGTATTTCCCAAAGGACAAGAATGAGAGTACCTACCCACACA
AGATGGGCGAACAGCTTCTTGGAGAACTACAAGTGAAGAAAAGAAAGCATTAGATCAAGCTAGTGAAGAGATTTGGAATG
ATTTTCGAGAAGCTGTGGAAGCACATTGACAAGTTAGAAAATATGTTGTGAGCTGGATCAAGCCTGGGATGACAATGATA
GAAATCTGTGAAAAATTGGAAGACTGTTCACGAAAGCTAATTAAAGAGAATGGATTAAATGCAGGCTTGGCATTTCCTAC
TGGGTGTTCTCTGAATAACTCTGCTGCCCATTATACTCCAAATGCTGGTAATACAACAGTATCACAGTATGTTGACATCT
GTAAGATAGATTTTGGAACACATATAAGTGGTAGGATTATTGACTGTGCTTTTACCATTACTTTTAATCCCAAATATGAT
ACATTATTAAAAGCTGTAAAGGATGCCACTAACACTGGAATAAAGTGTGCTGGAATTGATGTCCGTCTATGTGATGTTGG
TGAGGCCATCCAAGAAGTTATGGAATCCTAGGAGGTTGAAATAATGGGAAGACATATCAAGTGAAACCAATCTGTAACCT
AAATGGACATTCAATTGGGCGATATAGAATACATGCTGGGAAAACAGTGCCAATTGTGAAAGGAGAAGAGGCAACAAGAA
TAGAGGAAGGAGAAGGGTATGCCATTGAAACCTTTGGAAGCACAGGAAAAGGCGTTGTTCATGATGACATGGAATGTTCA
CATTATATGAAAAATCTTGATGTTGGACACGTGCCAATCAGGCTTCCAAGAACAAAACACTTGCTGAACGTCATCAATGA
AAACTTTGGCACCCTAGCCTTCTGCTGCAGGTGGCTGGATCACTTGGGAGAAAGTAAATACTTCATGGCTTTGAAGAATC
TGTGTGACTTGGGCATTGTAGATCCATATCCACCATCATGTGATATTAAAGGATCATATACAGCACAGTTTGAACATACC
ATACTGTTGTGTCCAACGTGTAAAGAAGTTGTCAGCAGAGGAGATGACTAT

Alignment

ORF - retro_cfam_1330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGVEEAASSGSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGAATAGQQEPDKESGASVDEVARQ
          .AGVEEAASSGSHLNGDLDP.DRE.GAAST.EEAAKKKR.K.K.SKGAATAG.QEPDKESGASVDEVARQ
Retrocopy VAGVEEAASSGSHLNGDLDPNDREDGAASTTEEAAKKKRWKNK-SKGAATAGKQEPDKESGASVDEVARQ

Parental  L-ERQALEEKERDDDDEDGDGDGDGATGKKKKKKKKKRGPKVQTDPPSVPICDLYPNGVFPKGQECEYPP
          L...QALEEKER..DD..........TG....KKKKKRGPKVQTDPPSVP.CDLYPNGVFPKGQE.EY.P
Retrocopy L<VKQALEEKER--DDDXXXXXXXXXTG----KKKKKRGPKVQTDPPSVPVCDLYPNGVFPKGQE*EYLP

Parental  TQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIK
          TQDGRTA.WRTTSEEKKALDQASEEIWNDFREA.EAH.QVRKYV.SWIKPGMTMIEICEKLEDCSRKLIK
Retrocopy TQDGRTASWRTTSEEKKALDQASEEIWNDFREAVEAH*QVRKYVVSWIKPGMTMIEICEKLEDCSRKLIK

Parental  ENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKA
          ENGLNAGLAFPTGCSLNN.AAHYTPNAG.TTV.QY.DICKIDFGTHISGRIIDCAFT.TFNPKYDTLLKA
Retrocopy ENGLNAGLAFPTGCSLNNSAAHYTPNAGNTTVSQYVDICKIDFGTHISGRIIDCAFTITFNPKYDTLLKA

Parental  VKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEI-DGKTYQVKPIRNLNGHSIGPYRIHAGKTVPIVK
          VKDATNTGIKCAGIDVRLCDVGEAIQEVMES.EVEI..GKTYQVKPI.NLNGHSIG.YRIHAGKTVPIVK
Retrocopy VKDATNTGIKCAGIDVRLCDVGEAIQEVMES*EVEI<NGKTYQVKPICNLNGHSIGRYRIHAGKTVPIVK

Parental  GGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRR
          G.EATR.EEGE.YAIETFGSTGKGVVHDDMECSHYMKN.DVGHVPIRLPRTKHLLNVINENFGTLAFC.R
Retrocopy GEEATRIEEGEGYAIETFGSTGKGVVHDDMECSHYMKNLDVGHVPIRLPRTKHLLNVINENFGTLAFCCR

Parental  WLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY
          WLD.LGESKY.MALKNLCDLGIVDPYPP.CDIKGSYTAQFEHTILL.PTCKEVVSRGDDY
Retrocopy WLDHLGESKYFMALKNLCDLGIVDPYPPSCDIKGSYTAQFEHTILLCPTCKEVVSRGDDY

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	0.04 RPM	56.03 RPM
SRP017611_brain	0.00 RPM	38.98 RPM
SRP017611_kidney	0.00 RPM	98.86 RPM
SRP017611_liver	0.00 RPM	36.84 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1330 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1330 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006353	1 retrocopy	retro_cfam_1330 ,
Monodelphis domestica	ENSMODG00000008173	1 retrocopy	retro_mdom_297,
Mus musculus	ENSMUSG00000036112	2 retrocopies	retro_mmus_3689, retro_mmus_770,
Otolemur garnettii	ENSOGAG00000008469	1 retrocopy	retro_ogar_2163,
Rattus norvegicus	ENSRNOG00000021881	2 retrocopies	retro_rnor_1707, retro_rnor_547,