RetrogeneDB ID: retro_rnor_579

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:48887514..48888429(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000018935
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tecr
• Ensembl ID: ENSRNOG00000021808
• Aliases: Tecr, Gpsn2, SC2
• Description: Trans-2,3-enoyl-CoA reductase [Source:UniProtKB/Swiss-Prot;Acc:Q64232]

Sequence

>retro_rnor_579
ATGAAGCACTACGAGGTGGATGCAAAGACGAGGGAGAAGCTGTGCTTCCTGGACAAGGTAGAGCCTCAGGCCACCATTTC
TGAAATCAAGACCCTTTTCACCAAGACACTCCCGCAGTGGTATCCTGCCCGCCAGTCCCTCCGCCTGGACCCCAAGGGGA
AGTCCCTGAAAGATGAAGATGTGTTGCAGAAGCTTCCTGTGGGCACCACAGCCACGCTCTACTTCCGGGACCTCGGGGCC
CAGATCAGCTGGGTGACGGTCTTCCTGACGGAGTATGCTGGGCCCCTTTTCATCTACCTGCTCTTCTACTTCCGGGTGCC
CTTCATTTATGGCCGCAAATATGACTTTACATCCAGTCAGCATATGGTGGTGCACCTCGCCTGCATGTGCCACTCCTTCC
ACTACATCAAGCGCCTGCTGGAGACTCTCTTTGTGCACCGAGTCTCTCACGGAACCATGCCCCTGCGAAACATCTTCAAA
AACTGCACCTACTACTGGGGCTTTGCTGCGTGGATGGCTTATTACATCAACCACCCTCTCTACACACCCCCTACCTATGG
AGTTCAGCAGGTTAAGCTGGCACTGGCCATTTTTGTGATCTGTCAGCTTGAGAACTTCTCTATCCACATGGCTCTCCGGG
ATCTTCGGCCAGCGGGGTCGAAAATCAGGAAGATCCCATACCCCACCAAGAACCCCTTCACCTGGCTGTTTCTGTTAGTG
TCCTGTCCCAATTACACTTACGAGGTCGGCTCCTGGATTGGCTTTGCCATCATGACACAGTGTGTCCCAGTGGCCCTCTT
CTCCCTGGTGGGCTTCACCCAGATGACTATCTGGGCCAAGGGCAAGCATCGCAGCTACCTGAAGGAGTTCCGTGACTACC
CACCCCTGCGCATGCCCATAATCCCCTTCCTGCTC

Alignment

ORF - retro_rnor_579 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKHYEVEIRDAKTREKLCFLDKVEPQATISEIKTLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPV
          MKHYEV...DAKTREKLCFLDKVEPQATISEIKTLFTKT.PQWYPARQSLRLDPKGKSLKDEDVLQKLPV
Retrocopy MKHYEV---DAKTREKLCFLDKVEPQATISEIKTLFTKTLPQWYPARQSLRLDPKGKSLKDEDVLQKLPV

Parental  GTTATLYFRDLGAQISWVTVFLTEYAGPLFIYLLFYFRVPFIYGRKYDFTSSRHTVVHLACMCHSFHYIK
          GTTATLYFRDLGAQISWVTVFLTEYAGPLFIYLLFYFRVPFIYGRKYDFTSS.H.VVHLACMCHSFHYIK
Retrocopy GTTATLYFRDLGAQISWVTVFLTEYAGPLFIYLLFYFRVPFIYGRKYDFTSSQHMVVHLACMCHSFHYIK

Parental  RLLETLFVHRFSHGTMPLRNIFKNCTYYWGFAAWMAYYINHPLYTPPTYGVQQVKLALAIFVICQLGNFS
          RLLETLFVHR.SHGTMPLRNIFKNCTYYWGFAAWMAYYINHPLYTPPTYGVQQVKLALAIFVICQL.NFS
Retrocopy RLLETLFVHRVSHGTMPLRNIFKNCTYYWGFAAWMAYYINHPLYTPPTYGVQQVKLALAIFVICQLENFS

Parental  IHMALRDLRPAGSKTRKIPYPTKNPFTWLFLLVSCPNYTYEVGSWIGFAIMTQCVPVALFSLVGFTQMTI
          IHMALRDLRPAGSK.RKIPYPTKNPFTWLFLLVSCPNYTYEVGSWIGFAIMTQCVPVALFSLVGFTQMTI
Retrocopy IHMALRDLRPAGSKIRKIPYPTKNPFTWLFLLVSCPNYTYEVGSWIGFAIMTQCVPVALFSLVGFTQMTI

Parental  WAKGKHRSYLKEFRDYPPLRMPIIPFLL
          WAKGKHRSYLKEFRDYPPLRMPIIPFLL
Retrocopy WAKGKHRSYLKEFRDYPPLRMPIIPFLL

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	0.72 RPM	258.90 RPM
SRP017611_kidney	0.28 RPM	88.90 RPM
SRP017611_liver	0.40 RPM	149.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_579 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000020013	1 retrocopy	retro_etel_1012,
Homo sapiens	ENSG00000099797	1 retrocopy	retro_hsap_3092,
Mus musculus	ENSMUSG00000031708	1 retrocopy	retro_mmus_1662,
Nomascus leucogenys	ENSNLEG00000013546	1 retrocopy	retro_nleu_124,
Pongo abelii	ENSPPYG00000009648	2 retrocopies	retro_pabe_2561, retro_pabe_3591,
Rattus norvegicus	ENSRNOG00000021808	1 retrocopy	retro_rnor_579 ,