RetrogeneDB ID: retro_rnor_2070

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:152428957..152429701(-)
• Located in intron of: ENSRNOG00000045592

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tubg1
• Ensembl ID: ENSRNOG00000020213
• Aliases: None
• Description: Tubulin gamma-1 chain [Source:UniProtKB/Swiss-Prot;Acc:P83888]

Sequence

>retro_rnor_2070
GAATGTGTGGTGGTTCTGGACAACATGGCCTTGAACATGATCAACATAGACTACCTGGACATCCAGAAACCATCTTTCTC
TCAGATCAACCAGCTGGTGTCCACTATCGTGTCAGCCAGCACCACCACCCTCCGCTACCCCAGACACATGAACAATTATT
TCATCGGCCTCATTGTCTCTCCCAGTCCCACCCCTTGGCTGCACTTCCTCATGACTGGCTATTCCTCCCTCACCACAGAA
GAGTAGTCAATGTCCAGCATGAGGAAGACAATGGTTCTGGATGTCATGAAGAGACTGCTACAGCCCAAGAACATGATATT
GTATACAGGCCAGGATCACCAGACCAACTACTGCTACATCGCCATCCTCAACATCATCCAGAGAATGGCGAACCCCACCT
AGGTCCTCAAGGACCTGCAGAGGATCTGGGAAAGGAAGTTGGCAATCTTCATCTCCTGGGGCCCAGCCATTCAGGAGGCC
CTGTCAAGGAAATCTCCCTAACTGCCCTCAGCCCACTGGGTCAGCGGGCTCATGAGGCGAATCACTAGTAACTCCTTGCT
TTTTGAAAGAATCTGTCACCAGTTTGACAAGCTGCAGAAATGGGAGGCCTTCATGGCACAGTTCTGCAAGGAGGGCATCT
TCAAGGATAATTTTGATGAGATTGTCACCTCTAGGGACATTGTACAGCAGCTGATTGACCAGTACCCTGCAACCACATGG
CCAGACTACATCACCCAGGAGCAA

Alignment

ORF - retro_rnor_2070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 55.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DCVVVLDNTALNLIATDRLHIQNPSFSQINQLVSTIMSASTTTLRYPGYMNNDLIGLIASLIPTPRLHFL
          .CVVVLDN.ALN.I..D.L.IQ.PSFSQINQLVSTI.SASTTTLRYP..MNN..IGLI.S..PTP.LHFL
Retrocopy ECVVVLDNMALNMINIDYLDIQKPSFSQINQLVSTIVSASTTTLRYPRHMNNYFIGLIVSPSPTPWLHFL

Parental  MTGYTPLTTDQ-SVASVRKTTVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQ
          MTGY..LTT...S..S.RKT.VLDVM.RLLQPKN....TG.D.QTN.CYIAILNIIQ....PT.V.K.LQ
Retrocopy MTGYSSLTTEE*SMSSMRKTMVLDVMKRLLQPKNMILYTGQDHQTNYCYIAILNIIQRMANPT*VLKDLQ

Parental  RIRERKLANFIPWGPASIQVALSRKSPYLPSAHRVSGLMMANHTSISSLFERTCRQFDKLRKREAFMEQF
          RI.ERKLA.FI.WGPA.IQ.ALSRKSP.LPSAH.VSGL.M...TS.S.LFER.C.QFDKL.K.EAFM.QF
Retrocopy RIWERKLAIFISWGPA-IQEALSRKSP*LPSAHWVSGL-MRRITSNSLLFERICHQFDKLQKWEAFMAQF

Parental  RKEDIFKDNFDEMDTSREIVQQLIDEYHAATRPDYISWGTQEQ
          .KE.IFKDNFDE..TSR.IVQQLID.Y.A.T.PDYI...TQEQ
Retrocopy CKEGIFKDNFDEIVTSRDIVQQLIDQYPATTWPDYI---TQEQ

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	27.97 RPM
SRP017611_kidney	0.00 RPM	23.10 RPM
SRP017611_liver	0.00 RPM	12.64 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2070 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2070 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2070 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004907	1 retrocopy	retro_cjac_4142,
Echinops telfairi	ENSETEG00000008542	1 retrocopy	retro_etel_496,
Homo sapiens	ENSG00000131462	1 retrocopy	retro_hsap_3725,
Gorilla gorilla	ENSGGOG00000010899	1 retrocopy	retro_ggor_2515,
Macaca mulatta	ENSMMUG00000016797	1 retrocopy	retro_mmul_1692,
Nomascus leucogenys	ENSNLEG00000011686	1 retrocopy	retro_nleu_71,
Pongo abelii	ENSPPYG00000008384	1 retrocopy	retro_pabe_3132,
Pan troglodytes	ENSPTRG00000009211	1 retrocopy	retro_ptro_2520,
Rattus norvegicus	ENSRNOG00000020213	2 retrocopies	retro_rnor_2070 , retro_rnor_2072,
Tupaia belangeri	ENSTBEG00000015835	3 retrocopies	retro_tbel_188, retro_tbel_3516, retro_tbel_955,