RetrogeneDB ID: retro_mmus_1962

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:112000203..112001301(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081037
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tdh
• Ensembl ID: ENSMUSG00000021953
• Aliases: None
• Description: L-threonine dehydrogenase [Source:MGI Symbol;Acc:MGI:1926231]

Sequence

>retro_mmus_1962
AAACAGGTGGTCAATGGGACTGCACAGAGCAAAGCCTCTAGCTGCCGGAAGCTTGTCTTGCCCTTGCAGTTTCTAGGCAC
CTCCCAGCACCGGATCCCAGCCGATGCCAACTTCTACTCCACCTCGATCTCAGAAGCTGAGCCTCCTCGGGTCTTGATCA
CAGGGGGTCTTGGCCAGCTGGGAGTAGGACTTGCTAACCTCCTGAGGAAACGATTTGGGAAGGACAATGTGATCCTATCA
GACATAAGGAAGCCCCCTGCTCATGTCTTCCACAGCGGCCCATTTGTTTATGCCAACATCTTGGATTACAAGAGCCTCCG
TGAGATCGTGGTGAACCACCGTATCAGCTGGCTGTTTCACTACAGTGCCCTGCTGAGTGCCATGGGAAAGGCAAATGTGT
CCTTAGCCAAAGATGTGAATATAACTGGACTGCATAACGTTCTAGATGTTGCAGCTGAATACAACGTGAGATTGTTTGTG
CCCAGCACGATTGAAGCCTTTGAACCTACCTCTCCCCAGAACCCTGCACCCGATCTCTGTATTCAAAGGCCTAGGACCAT
CTATGGGGTATCCAAGGTCCACACGGAGCTCATGGGAGAATACTATTATTACCGGTACAGGTTAGATTTCCGGTGCCTGC
GATATCCTGGAATCATTTCTGCAGATTCCCAGTCTGGAGGAGGAACAACTGACTACGCTGTCCAGATTTTCCACGCTGCA
GCAAAGAACGGCACATTCGAATGCAACCTCGAGGCCGGCACCAGGCTCCCAATGATGTACATCAGTGACTGTCTCAGGGC
CACCCTGGAGGTCATGGAAGCCCCTGCCGAGCGCCTGTCCATGAGAACCTACAACATCGGCACCATGAGCTTCACCCCTG
AAGAGCTGGCCCAGGCGCTCCGCAAGCATGCTCCTGACTTCCAGATCACCTACTGCGTGGATCCCCTCCGACAAGCCATA
GCGGAGAGCTGGCCCATGATTCTAGATGACAGCAATGCTCGGAAGGACTGGGGCTGGAAGCATGACTTTGATCTTCCAGA
GTTGGTGGCTACGATGCTCAACTTCCACTGCGTCAGCACCAGAGTTGCCCAAGTGAAC

Alignment

ORF - retro_mmus_1962 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.45 %
• Parental protein coverage: 98.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQVVNGTAQSKASSCRKLVLPLKFLGTSQHRIPADANFHSTSISEAEPPRVLITGGLGQLGVGLANLLRK
          KQVVNGTAQSKASSCRKLVLPL.FLGTSQHRIPADANF.STSISEAEPPRVLITGGLGQLGVGLANLLRK
Retrocopy KQVVNGTAQSKASSCRKLVLPLQFLGTSQHRIPADANFYSTSISEAEPPRVLITGGLGQLGVGLANLLRK

Parental  RFGKDNVILSDIRKPPAHVFHSGPFVYANILDYKSLREIVVNHRISWLFHYSALLSAVGEANVSLARDVN
          RFGKDNVILSDIRKPPAHVFHSGPFVYANILDYKSLREIVVNHRISWLFHYSALLSA.G.ANVSLA.DVN
Retrocopy RFGKDNVILSDIRKPPAHVFHSGPFVYANILDYKSLREIVVNHRISWLFHYSALLSAMGKANVSLAKDVN

Parental  ITGLHNVLDVAAEYNVRLFVPSTIGAFGPTSPRNPAPDLCIQRPRTIYGVSKVHTELMGEYYYYRYGLDF
          ITGLHNVLDVAAEYNVRLFVPSTI.AF.PTSP.NPAPDLCIQRPRTIYGVSKVHTELMGEYYYYRY.LDF
Retrocopy ITGLHNVLDVAAEYNVRLFVPSTIEAFEPTSPQNPAPDLCIQRPRTIYGVSKVHTELMGEYYYYRYRLDF

Parental  RCLRYPGIISADSQPGGGTTDYAVQIFHAAAKNGTFECNLEAGTRLPMMYISDCLRATLEVMEAPAERLS
          RCLRYPGIISADSQ.GGGTTDYAVQIFHAAAKNGTFECNLEAGTRLPMMYISDCLRATLEVMEAPAERLS
Retrocopy RCLRYPGIISADSQSGGGTTDYAVQIFHAAAKNGTFECNLEAGTRLPMMYISDCLRATLEVMEAPAERLS

Parental  MRTYNISAMSFTPEELAQALRKHAPDFQITYCVDPLRQAIAESWPMILDDSNARKDWGWKHDFDLPELVA
          MRTYNI..MSFTPEELAQALRKHAPDFQITYCVDPLRQAIAESWPMILDDSNARKDWGWKHDFDLPELVA
Retrocopy MRTYNIGTMSFTPEELAQALRKHAPDFQITYCVDPLRQAIAESWPMILDDSNARKDWGWKHDFDLPELVA

Parental  TMLNFHGVSTRVAQVN
          TMLNFH.VSTRVAQVN
Retrocopy TMLNFHCVSTRVAQVN

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	0.00 RPM	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.13 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.05 RPM
SRP007412_testis	0.00 RPM	1.60 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1962 was not detected

EST

No EST(s) were mapped for retro_mmus_1962 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_78638	1025 libraries	13 libraries	3 libraries	16 libraries	15 libraries
TSS #2	TSS_78639	1031 libraries	13 libraries	25 libraries	3 libraries	0 libraries

The graphical summary, for retro_mmus_1962 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002579	1 retrocopy	retro_chof_1442,
Callithrix jacchus	ENSCJAG00000004107	1 retrocopy	retro_cjac_3935,
Mus musculus	ENSMUSG00000021953	1 retrocopy	retro_mmus_1962 ,