RetrogeneDB ID: retro_mmus_1662

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:73870433..73871350(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tecr
• Ensembl ID: ENSMUSG00000031708
• Aliases: Tecr, 2410016D23Rik, A230102P12Rik, AI173355, D17Ertd178e, Gpsn2, SC2
• Description: trans-2,3-enoyl-CoA reductase [Source:MGI Symbol;Acc:MGI:1915408]

Sequence

>retro_mmus_1662
ATGAAGCACTATGAGGTGGGGGTTCGGGATGCAAAGACAAGAGAGAAGCTGTGGTTCGTGGACAAGGTAGAGCCTCAGGC
CACCATTTCTGAAATCAAGACCCTTTTCACCAAGACACATCCACAGTGGTATCCTGCCAGCCAGTCCCTCCGCCTGGACC
CCAAGGGGAAGTCCCTGAAAGATGAAGATGTCTTGCAGAAACTTCCTGTGGGCACCACAGCCACGCTCTACTTCTGGGAC
CTCAGGGCCCAGATCAGCTGGGTGACGGTTTTCCTGATGGAGTATGCCGGCCCCCTTTTCATCTACCTGCTCTTCTACCG
GGTACCCTTCATTTATGGCCGCACAAACAACTTTACATCCAGTCGGCATATGGTGGTGCCCCTCACCTGCATGTGCCACT
CATTCCACTACATCAAATGCCTGCTGGAGACTCTCTTCGTGCACCGATTCTCTCACGGAACCGCGCCTTTGCAAAACATC
TTCAAAAACTGCACCTACAATTGGGGCTTTGCTGCATGGATGGCTTCTTACATCAACCACCCTGTCTACACACCCCCTAC
CTATGGAGTTCAGCAGGTTAAGCTGGCACTGGCCGTTTTTGTGATCTACCAGCTTGGGAACCTCTCCATCCACATGGTTC
TTCGGGACCTTCGGCTGGGTCGAAAACCAGGAAGTTCCCATACCCCTCCAAGAACCCTTTCACCTGGCTGTTTCTGTTGG
TGTCCTGTCCCAGCTGCACTTATGAGGTGCGCTCCTGGATTGGCTTTGCCATCTTGACTCAGTGTGTCCCAGTGGCCCTC
TTCTCCCTGGTGGGCTTCACCCAGATGACTATCTGGGCCAAGTGCAAGCATCACAGCTACCTGTAGGAGTTCTGCAACTA
CCTGCCCCTCTGCATGCCCATTATCCCCTTCCTGCTC

Alignment

ORF - retro_mmus_1662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKHYEVEIRDAKTREKLCFLDKVEPQATISEIKTLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPV
          MKHYEV..RDAKTREKL.F.DKVEPQATISEIKTLFTKTHPQWYPA.QSLRLDPKGKSLKDEDVLQKLPV
Retrocopy MKHYEVGVRDAKTREKLWFVDKVEPQATISEIKTLFTKTHPQWYPASQSLRLDPKGKSLKDEDVLQKLPV

Parental  GTTATLYFRDLGAQISWVTVFLTEYAGPLFIYLLFYFRVPFIYGRKYDFTSSRHTVVHLACMCHSFHYIK
          GTTATLYF.DL.AQISWVTVFL.EYAGPLFIYLLFY.RVPFIYGR...FTSSRH.VV.L.CMCHSFHYIK
Retrocopy GTTATLYFWDLRAQISWVTVFLMEYAGPLFIYLLFY-RVPFIYGRTNNFTSSRHMVVPLTCMCHSFHYIK

Parental  RLLETLFVHRFSHGTMPLRNIFKNCTYYWGFAAWMAYYINHPLYTPPTYGVQQVKLALAVFVICQLGNFS
          .LLETLFVHRFSHGT.PL.NIFKNCTY.WGFAAWMA.YINHP.YTPPTYGVQQVKLALAVFVI.QLGN.S
Retrocopy CLLETLFVHRFSHGTAPLQNIFKNCTYNWGFAAWMASYINHPVYTPPTYGVQQVKLALAVFVIYQLGNLS

Parental  IHMALRDLRPAGSK-TRKIPYPTKNPFTWLFLLVSCPNYTYEVGSWIGFAILTQCVPVALFSLVGFTQMT
          IHM.LRDLR..G.K.TRK.PYP.KNPFTWLFLLVSCP..TYEV.SWIGFAILTQCVPVALFSLVGFTQMT
Retrocopy IHMVLRDLR-LGRK<TRKFPYPSKNPFTWLFLLVSCPSCTYEVRSWIGFAILTQCVPVALFSLVGFTQMT

Parental  IWAKGKHRSYLKEFRDYPPLRMPIIPFLL
          IWAK.KH.SYL.EF..Y.PL.MPIIPFLL
Retrocopy IWAKCKHHSYL*EFCNYLPLCMPIIPFLL

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
SRP007412_brain	0.37 RPM	222.18 RPM
SRP007412_cerebellum	0.17 RPM	306.29 RPM
SRP007412_heart	0.16 RPM	289.11 RPM
SRP007412_kidney	0.25 RPM	157.10 RPM
SRP007412_liver	0.08 RPM	190.61 RPM
SRP007412_testis	0.05 RPM	41.62 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1662 was not detected

EST

No EST(s) were mapped for retro_mmus_1662 retrocopy.

TSS

No TSS is located nearby retro_mmus_1662 retrocopy 5' end.

Lab

retro_mmus_1662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1662 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,