RetrogeneDB ID: retro_rnor_430

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:44323415..44324257(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nt5c2
• Ensembl ID: ENSRNOG00000020179
• Aliases: None
• Description: None

Sequence

>retro_rnor_430
TATCACCGGGTGTTTGTGAACCGAAGTTTAGCCATGGAAAAAATAAAGTGTTTTGGGTTTAACATGGATTATACCCTGGC
TGTGTACAAGTCTCCGGAATATGAATCCCTTGGCTTTGAGCTTACTGTGGAGAGATTAGTTTCCATCAGCTATCCTCAGG
ATAGCTCAACTTTGCATACGATTCTACATTCCCTACCAGAGGGCTCGTCTTTGACACACTCTATGGAAATCTCTTGAAAG
TTGATGCCTATGGAAACCTCTTCGTTTGTGCACATGGATTTAACTTCATAAGAGGACCAGAAACTAGAGAGCAGTATCCA
AATAAATTTATCCCATGAGATGATACTGAACAGTTTTACATTCTGAACACACTATTCGACCTTCCAGAGACCTACCTGTT
GACCTGCCTAGTAGAACTTTTTACTAATTGTCCCAGATATACCAGTTGTGACACAGGATTTAAAGATGGGGACCTTTTCA
TGTCCTACTGGAGTATGTTCCAGGATGTAAGAGACGCAGTGGACTAGGTCCATTACAAGGGTTCCCTTAACTCCGTAAGA
GTTGAAAATCTTGAGAAGTATGTAGTCAAAGATGGCAAGTTGCGGTTGCTTCTGAGCCGAATGAAGGAAGTGGGGAAAGT
GTTTCTGGCCCCTAACAGTGACTATAAATACACAGATAAAATCATGGCTTACCTGTTTGATTTCCCACATGGCCCCAAGC
CTGGGAGCTCCCATCGGCCGTGGCAGTCCTACTTTGATCTGATTTTGGTGGATGCACGGAAACCGCTCTTTTTTGGAGAA
GGCACAGTGCTGTGTCAGGTGGACACTGAAAACTGAAAATTG

Alignment

ORF - retro_rnor_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 53.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FYRVFVNRSLAMEKIKCFGFDMDYTLAVYKSPEYESLGFELTVERLVSIGYPQEL-LNFAYDSTFPTRGL
          ..RVFVNRSLAMEKIKCFGF.MDYTLAVYKSPEYESLGFELTVERLVSI.YPQ...LNFAYDSTFPTRGL
Retrocopy YHRVFVNRSLAMEKIKCFGFNMDYTLAVYKSPEYESLGFELTVERLVSISYPQDS<LNFAYDSTFPTRGL

Parental  VFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQYPNKFIQRDDTERFYILNTLFNLPETYLLACLVD
          VFDTLYGNLLKVDAYGNL.VCAHGFNFIRGPETREQYPNKFI..DDTE.FYILNTLF.LPETYLL.CLV.
Retrocopy VFDTLYGNLLKVDAYGNLFVCAHGFNFIRGPETREQYPNKFIP*DDTEQFYILNTLFDLPETYLLTCLVE

Parental  FFTNCPRYTSCDTGFKDGDLFMSYRSMFQDVRDAVDWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMK
          .FTNCPRYTSCDTGFKDGDLFMSY.SMFQDVRDAVD.VHYKGSL....VENLEKYVVKDGKL.LLLSRMK
Retrocopy LFTNCPRYTSCDTGFKDGDLFMSYWSMFQDVRDAVD*VHYKGSLNSVRVENLEKYVVKDGKLRLLLSRMK

Parental  EVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTG
          EVGKVFLA.NSDYKYTDKIM.YLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVL.QVDT...
Retrocopy EVGKVFLAPNSDYKYTDKIMAYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLCQVDTEN*

Parental  KL
          KL
Retrocopy KL

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
SRP017611_brain	0.22 RPM	35.44 RPM
SRP017611_kidney	0.98 RPM	90.30 RPM
SRP017611_liver	0.27 RPM	22.26 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_430 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_430 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_430 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010354	1 retrocopy	retro_cfam_684,
Choloepus hoffmanni	ENSCHOG00000004098	1 retrocopy	retro_chof_280,
Microcebus murinus	ENSMICG00000012316	1 retrocopy	retro_mmur_1476,
Rattus norvegicus	ENSRNOG00000020179	1 retrocopy	retro_rnor_430 ,
Tupaia belangeri	ENSTBEG00000017707	4 retrocopies	retro_tbel_2188, retro_tbel_3201, retro_tbel_3465, retro_tbel_3467,