RetrogeneDB ID: retro_rnor_1929

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:152207147..152208473(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tead2
• Ensembl ID: ENSRNOG00000020695
• Aliases: None
• Description: transcriptional enhancer factor TEF-4 [Source:RefSeq peptide;Acc:NP_001100982]

Sequence

>retro_rnor_1929
ATGGAGGATCCCCGGACTGGGGCCCCCCTGGATGATGGCGGGGGGCTGGACAGGTAGTAAGGAAGGCAGTGAGGAGGGCA
CCGGAGGCAGTGAGGGTGTTGGAGGTGATGGGAGCCCCCATGAAGAAGGTGTGTGGAGCCCTGACATCGAGCAGAGTTTT
CAGGAGGCCCTGACAATCTACCCTCCCTGTGGCCGTCGCAAGATCATCTTGTCAGATGAGGGCAAGATGTATGACTGGAA
CGAACCCATTGCCCATTACAACAAGCTGAGGAAGGGAAGACCAGAACTCAAAAGCAGGTCTCTAGTCACATCCAGGTTTT
GGCTCGAAGGAAATCGAGAGAAATTCAGTCCAAGCTGAAGGACCAAGTCTCCAAGGACAAGGCCTTCCAGACGATGGCCA
CCATGTCTTCGGCACAACTCATCTCTGCACCTTCCCTCCAGGCCAAGCTGGGTCCTTCTAGCCCTCAGGCCACCGAGCTT
TTCCAGTTCTGGTCAGGGAGCTCTGGGCCAACATGGAATGTTCCAGACATGAAGCCCTTCTCACAAGCACCATTCTCCAT
GTCACTGACGCCCCCAGCCACTGACCTACCAAGGTACAAGCCGCCCCCAGCCCTCTCACTCCTGCCCCCACCTGCTCCTC
TCCCCCAGTCTGGCAGGTTCCGGCCCTGGGCACTGTGCACCTGCAGCTGGTAGAGTTCTCAGCGTTTGTGGAGCCACCAG
ATGCAGTTGACTCGTTCCAGAGTCATCTGTTTGTCCACATCAGTCAGCAGTGCCCCAGCCCTGGAGCCCCACCTCTGGAG
AGTGTGGACGTGCGGCAGATCTATGACAAATTCCCTGAGAAAAAGGGCGGTCTCCCGGAGCTGTATGACCGGGGGCCACC
ACATGCATTTTTCCTGGTCAAGCTCTGGGCAGACCTGAACTGGGACCCCAAGTGCCGAGGAGGCAGGGAGCAGTGGAGGC
GCTGGTGGCTTCTATGGAGTGAGCAGTCAGTAGGAGAGCCAGGAGCTCATGACACTTACCTGCTCCTCCAAGGTCTGCTC
CTTTGGCAAGCAAGTGGTGGAGAAGGTGGAGACTGAGCGGGCCTAGCTGGAGGGCAGGTGCTTTGTGTACCGCCTGCTGC
GCTCTCCCATGTGTAAATACCTGGTTAACTTCCTGCACAAGCTCCATCTGCTGCCTGAACGCTACATGATGAACAGTGTC
CTGGAGAACTTCACTGTCCTCCAGGTCGTGACAAACAGGGACACTCCGGAACTACTGCTGTGTACTGCCTACGTCTTTGA
AGTCTCCACCAGAACTCAGCACCACATCTACCACCTGGTCAGAGAG

Alignment

ORF - retro_rnor_1929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGDPRTGAPLDDGGG-WTGSEEGSEEGTGGSEGVGGDGSPDAEGVWSPDIEQSFQEALAIYPPCGRRKII
          M.DPRTGAPLDDGGG.WTGS.EGSEEGTGGSEGVGGDGSP..EGVWSPDIEQSFQEAL.IYPPCGRRKII
Retrocopy MEDPRTGAPLDDGGG>WTGSKEGSEEGTGGSEGVGGDGSPHEEGVWSPDIEQSFQEALTIYPPCGRRKII

Parental  LSDEGKMYGRNELIARYIKLRTG-KTRTRKQVSSHIQVLARRKSREIQSKLKDQVSKDKAFQTMATMSSA
          LSDEGKMY..NE.IA.Y.KLR.G.KTRT.KQVSSHIQVLARRKSREIQSKLKDQVSKDKAFQTMATMSSA
Retrocopy LSDEGKMYDWNEPIAHYNKLRKG<KTRTQKQVSSHIQVLARRKSREIQSKLKDQVSKDKAFQTMATMSSA

Parental  QLISAPSLQAKLGPSGPQATELFQFWSGSSGPTWNVPDVKPFSQAPFSMSLTPPATDLPGYEPPPALSPL
          QLISAPSLQAKLGPS.PQATELFQFWSGSSGPTWNVPD.KPFSQAPFSMSLTPPATDLP.Y.PPPALS.L
Retrocopy QLISAPSLQAKLGPSSPQATELFQFWSGSSGPTWNVPDMKPFSQAPFSMSLTPPATDLPRYKPPPALSLL

Parental  PPPAP-SPPAWQARALGTARLQLVEFSAFVEPPDAVDSFQRHLFVHISQQCPSPGAPPLESVDVRQIYDK
          PPPAP.SPP.WQ..ALGT..LQLVEFSAFVEPPDAVDSFQ.HLFVHISQQCPSPGAPPLESVDVRQIYDK
Retrocopy PPPAP<SPPVWQVPALGTVHLQLVEFSAFVEPPDAVDSFQSHLFVHISQQCPSPGAPPLESVDVRQIYDK

Parental  FPEKKGGLRELYDRGPPHAFFLVKFWADLNWG-PSAEEAGNSGGAGGFYGVSSQYESRELMTLTCSSKVC
          FPEKKGGL.ELYDRGPPHAFFLVK.WADLNW..PSAEEAG.SGGAGGFYGVSSQ.ES.ELMTLTCSSKVC
Retrocopy FPEKKGGLPELYDRGPPHAFFLVKLWADLNWD>PSAEEAGSSGGAGGFYGVSSQ*ESQELMTLTCSSKVC

Parental  SFGKQVVEKVETERAQLEGGRFVYRLLRSPMCEYLVNFLHKLRQLPERYMMNSVLENFTILQVVTNRDTQ
          SFGKQVVEKVETERA.LEG..FVYRLLRSPMC.YLVNFLHKL..LPERYMMNSVLENFT.LQVVTNRDT.
Retrocopy SFGKQVVEKVETERA*LEGRCFVYRLLRSPMCKYLVNFLHKLHLLPERYMMNSVLENFTVLQVVTNRDTP

Parental  ELLLCTAYVFEVSTSERGAQHHIYRLVRD
          ELLLCTAYVFEVST.....QHHIY.LVR.
Retrocopy ELLLCTAYVFEVSTR---TQHHIYHLVRE

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	0.86 RPM
SRP017611_kidney	0.00 RPM	1.33 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_1929 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1929 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1929 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000016184	1 retrocopy	retro_lafr_1143,
Otolemur garnettii	ENSOGAG00000010067	2 retrocopies	retro_ogar_2638, retro_ogar_3448,
Rattus norvegicus	ENSRNOG00000020695	1 retrocopy	retro_rnor_1929 ,