RetrogeneDB ID: retro_rnor_2446

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:30197063..30197776(+)
• Located in intron of: ENSRNOG00000007197

Retrocopy information

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

Parental gene information

• Parental gene symbol: Anxa7
• Ensembl ID: ENSRNOG00000007136
• Aliases: None
• Description: annexin A7 [Source:RefSeq peptide;Acc:NP_569100]

Sequence

>retro_rnor_2446
GGTGGCTACCCAGGAGCTGGAGGCTACCCCCATACCTGGAGGTTATCCAGCCCCTGGGGTTTGAATCCAGGGGGTGCTCC
AGCCTATCCTGGAGGCCAAGGTTTTGGGGCCCCACCCAGTGGAGCAGGCTTTTCTGGCAATCCACAGCCACCCGCACATC
TTGTGGTGGTGGACCAGCCCAGGTTCCAGTATCAGGTGGCTTTCCCAGAGGACAGAGGCTGTGTCAGTACCCTGCAGGGC
AAGCTCCCTACCTGGGCCATCCTGCTGTGATGACTCAGGGCATCCAAGGAACAATCCGCCCAGTCTCCAACTTTGATGCT
TTGAGAGGTGCAGAAATTCTCCGCAAAGCAATGAAAGGGTTTGGGACAGACGGGCAAGCAATTGTGGATGTTGTGTCTAA
CCATCCCAATGACCAGAGGCGACAAATTAAAGCGGCCTTTAAGAACATGTATGGCAAGGATTTAATTAAAGATCTCGAGT
TAGAGTTGAGTGGAAATATGGAAGAATTAATCTTTGCCCTGTTCATGCCTTCTACATACTACGATGCCTGGAGTTTATGG
AAGGCAGTGCAGGGAGCTAGAACTCAAGAACGTGTATTGATAGAGATTTTGTGCAAAGGAACAAAACAAGAAATTCAAGA
CATTTTGAGATATCATCAATTAGAATTTGGATGAGACCTTGAGAAGGACACTATGTCGGATACCTCGGGACAT

Alignment

ORF - retro_rnor_2446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.01 %
• Parental protein coverage: 50.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGYPSPGGYP-APGGY--PGT-LNPGGPPSYPGGQGFGAPPGGAGFSGYPQPPAQ-SYGGGPAQVPVPGG
          GGYP..GGYP..PGGY..PG..LNPGG.P.YPGGQGFGAPP.GAGFSG.PQPPA..S.GGGPAQVPV.GG
Retrocopy GGYPGAGGYP>IPGGYPAPGV<LNPGGAPAYPGGQGFGAPPSGAGFSGNPQPPAH<SCGGGPAQVPVSGG

Parental  FPGGQMPSQYPGGQSPYPGQPAAMTQGTQGTIRPASNFDAMRDAEILRKAMKGFGTDEQAIVDVVSNRSN
          FP.GQ...QYP.GQ.PY.G.PA.MTQG.QGTIRP.SNFDA.R.AEILRKAMKGFGTD.QAIVDVVSN..N
Retrocopy FPRGQRLCQYPAGQAPYLGHPAVMTQGIQGTIRPVSNFDALRGAEILRKAMKGFGTDGQAIVDVVSNHPN

Parental  DQRQQIKAAFKTMYGKDLIKDLKSELSGNMEELILALFMPPTYYDAWSLRKAIQGAGTQERVLIEILCTR
          DQR.QIKAAFK.MYGKDLIKDL..ELSGNMEELI.ALFMP.TYYDAWSL.KA.QGA.TQERVLIEILC..
Retrocopy DQRRQIKAAFKNMYGKDLIKDLELELSGNMEELIFALFMPSTYYDAWSLWKAVQGARTQERVLIEILCKG

Parental  TNQEIRDIVRCYQLEFGRELERDIRSDTSGH
          T.QEI.DI.R..QLEFG..LE.D..SDTSGH
Retrocopy TKQEIQDILRYHQLEFG*DLEKDTMSDTSGH

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	0.00 RPM	41.84 RPM
SRP017611_kidney	0.00 RPM	39.08 RPM
SRP017611_liver	0.00 RPM	7.67 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2446 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2446 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2446 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014749	1 retrocopy	retro_cfam_1107,
Callithrix jacchus	ENSCJAG00000001720	3 retrocopies	retro_cjac_1288, retro_cjac_2174, retro_cjac_860,
Microcebus murinus	ENSMICG00000013143	2 retrocopies	retro_mmur_404, retro_mmur_884,
Pteropus vampyrus	ENSPVAG00000013001	1 retrocopy	retro_pvam_1365,
Rattus norvegicus	ENSRNOG00000007136	1 retrocopy	retro_rnor_2446 ,
Ictidomys tridecemlineatus	ENSSTOG00000012433	1 retrocopy	retro_itri_1796,