RetrogeneDB ID: retro_rnor_2771

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:9361247..9362076(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000048608
• Aliases: None
• Description: None

Sequence

>retro_rnor_2771
ATGAAGCAATTAGCATCCGACTCTCCCTGTGCCTCAGCCGTTATGGGGACCACTACCTAGGTGCAAGCGGCACCGACTGC
TCTTGAACAGCTGGACAGATAGCAGATGTGAAAGGCAGTGGAAGTTCGGTTTGATCACTCCAAGTCCAAAAAAAAATAAT
AATGAATTGCTGTTGAATGGGAGTGAAAATTTATTTTTAATGGTGATACTATGGAAAATTCCAGAGAAAGAATGTCGGGT
CAGAGTGTCTTTACCTCATAGGATTCTCTCAGAATTCTCAGAAGTCTGTCTGTTTACCAAAGATGAATATAATTCACCTG
AACAGGCAGAAGGTTTCTATAAAAAAGCTTTTGAAAAAACATGGAGTAAACACTATCAAATTATCCCCTTTAAAATGTTA
AAAACTGAATATAAAGCCTATGAAACCAACCTCTGCCTCCTGAGTAACTTTGATGTTTTTATTACCGAAGAAAGAATTCG
GCGGCATTTGCCCAGGCAGGTAGGAAGGCATTTCTGTCAAAGGAAGAAAGTTCTAGTATCTGTAAACCTTCTGGCAAAGA
ATCTGTCCAAAGAGATTATCCGATGTATCACAGGGACTGTCTTAAACATCTCTAAGCGTGTTTCTTGCAGTATTGTCCAT
ATTGGTCACACTGGAATGGAGATTCAGCACATCATTGAAAACATCCTGACTGTCTCAGAAATGCTTTCAGAAAAATTGCC
AGAGAAATGGCAGAGTGTGAAACTCTTGTTCCTGAAATCTGAGAAGTTGGCTTCCCTTCCCATATTTTCCTCATTTGTCG
CATCTCAGGACAAAAACATTGCTTCCTTC

Alignment

ORF - retro_rnor_2771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.93 %
• Parental protein coverage: 59.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKCLASESPDASAATATTTEVQAEPTALEQLDREQIRKAVEVLFDNSKS-RKNNELLL-NGSENLFLMVI
          MK.LAS.SP.ASA...TTT.VQA.PTALEQLDR.Q..KAVEV.FD.SKS....N..LL.NGSENLFLMVI
Retrocopy MKQLASDSPCASAVMGTTT*VQAAPTALEQLDR*QM*KAVEVRFDHSKS>XXXNNELLLNGSENLFLMVI

Parental  LWKIPKKELRIRVSLPHSILSESSEVCLFTKDECDSPEQTEGFY-KKLLKKHGVNTISQIIP-FKTLKTE
          LWKIP.KE.R.RVSLPH.ILSE.SEVCLFTKDE..SPEQ.EGFY.KKLLKKHGVNTI....P.FK.LKTE
Retrocopy LWKIPEKECRVRVSLPHRILSEFSEVCLFTKDEYNSPEQAEGFY>KKLLKKHGVNTI-KLSP<FKMLKTE

Parental  YKAYEAKLRLLGSFDVFIADERIRRHLPTHIGRHFYQRKKVPVSVNLLAKNLSKEINRTITGTVLNISKR
          YKAYE..L.LL..FDVFI..ERIRRHLP...GRHF.QRKKV.VSVNLLAKNLSKEI.R.ITGTVLNISKR
Retrocopy YKAYETNLCLLSNFDVFITEERIRRHLPRQVGRHFCQRKKVLVSVNLLAKNLSKEIIRCITGTVLNISKR

Parental  GSCSTIRIGHTGMEIQHIIENILTVSEMLSEKLPEKWQSVKLLFLKTEKSVSLPIFSSFVTSQDENSASF
          .SCS...IGHTGMEIQHIIENILTVSEMLSEKLPEKWQSVKLLFLK.EK..SLPIFSSFV.SQD.N.ASF
Retrocopy VSCSIVHIGHTGMEIQHIIENILTVSEMLSEKLPEKWQSVKLLFLKSEKLASLPIFSSFVASQDKNIASF

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	4.46 RPM
SRP017611_kidney	0.00 RPM	4.95 RPM
SRP017611_liver	0.00 RPM	2.08 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2771 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2771 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018865	2 retrocopies	retro_cfam_1937, retro_cfam_691,
Choloepus hoffmanni	ENSCHOG00000010827	2 retrocopies	retro_chof_1617, retro_chof_852,
Callithrix jacchus	ENSCJAG00000008375	1 retrocopy	retro_cjac_2154,
Cavia porcellus	ENSCPOG00000010630	3 retrocopies	retro_cpor_1262, retro_cpor_276, retro_cpor_822,
Loxodonta africana	ENSLAFG00000013664	1 retrocopy	retro_lafr_364,
Myotis lucifugus	ENSMLUG00000000784	1 retrocopy	retro_mluc_1309,
Monodelphis domestica	ENSMODG00000029494	2 retrocopies	retro_mdom_1240, retro_mdom_573,
Otolemur garnettii	ENSOGAG00000015151	1 retrocopy	retro_ogar_2604,
Rattus norvegicus	ENSRNOG00000048608	1 retrocopy	retro_rnor_2771 ,
Sarcophilus harrisii	ENSSHAG00000016705	1 retrocopy	retro_shar_836,