RetrogeneDB ID: retro_mmus_1961

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:108948805..108950230(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000063684
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hadhb
• Ensembl ID: ENSMUSG00000059447
• Aliases: Hadhb, 4930479F15Rik, Mtpb, TP-beta
• Description: hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit [Source:MGI Symbol;Acc:MGI:2136381]

Sequence

>retro_mmus_1961
ATGACTACCATCTTGACTTCCACTTTTAGAAACTTGTCAACTACATCAAAATGGGCTCTCAGATCTTCTATAAGACCTCT
GAGCTGTTCTTCCCAACTGCACTCTGCCCCAGCTGTCCAGACCAAGTCAAAGAAGACTTTAGCAAAACCCAATATGAAGA
ATATTGTGGTGGTGGAAGGGGTCCGCATTCCATTTCTGCTATCAGGCACTTCGTATAAAGACCTAATGCCACATGACTTG
GCTAGAGCTGCACTTTCGGGTTTGTTGCATCGGACCAATATTCCAAAGGATGTTGTTGATTATATCATCTTTGGTACAGT
TATTCAGGAAGTGAAAACAAGCAATGTGGCTAGAGAGGCTGCCCTGGGAGCTGGCTTCTCTGATAAGACTCCGGCTCACA
CTGTCACCATGGCTTGTATCTCTTCAAACCAAGCCATGACCACAGCTGTTGGTCTGATAGCTTCTGGCCAGTGTGATGTC
GTCGTGGCTGGTGGTGTTGAGTTAATGTCTGATGTCCCTATTCGTCATTCAAGAAATATGAGGAAAATGATGCTTGATCT
CAATAAAGCCAAGACTCTGGGCCAGCGCCTGTCCTTACTCAGTAAATTCAGATTGAATTTTCTGTCCCCTGAGCTCCCTG
CAGTGGCTGAGTTCTCCACTAATGAGACCATGGGCCACTCTGCAGACCGACTGGCTGCTGCCTTTGCTGTTTCTCGAATG
GAACAGGATGAATATGCACTGCATTCTCATAGTCTGGCCAAGAAGGCACAGGATGAAGGACACCTTTCTGATATTGTACC
CTTCAAAGTACCAGGAAAGGACACAGTTACCAAAGATAATGGGATCCGTCCTTCCTCACTGGAGCAAATGGCCAAACTAA
AACCTGCGTTCATCAAACCCTATGGCACAGTGACAGCTGCAAATTCTTCTTTCCTGACTGATGGCGCTTCTGCGATGCTA
ATCATGTCAGAGGACAGAGCTCTGGCCATGGGTTATAAACCAAAGGCATATTTGAGGGATTTTATATATGTGTCCCAGGA
TCCGAAAGATCAGCTTTTACTCGGACCAACATATGCTACTCCAAAAGTTTTAGAAAAGGCAGGGTTAACCATGAATGATA
TCGATGCTTTTGAATTTCATGAAGCCTTCTCAGGCCAGATTTTAGCTAACTTTAAAGCCATGGATTCTGATTGGTTTGCA
CAAAACTACATGGGTAGGAAAACCAAGGTTGGATCACCTCCTCTGGAGAAGTTTAATATCTGGGGCGGATCACTGTCTCT
GGGGCACCCTTTTGGAGCCACTGGCTGTCGGCTGGTCATGGCAGCTGCCAACAGACTGAGGAAGGATGGAGGCCAGTATG
CTTTAGTGGCTGCCTGTGCAGCTGGAGGACAGGGTCATGCTATGATTGTGGAAGCTTACCCCAAA

Alignment

ORF - retro_mmus_1961 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTILTSTFRNLSTTSKWALRSSIRPLSCSSQLHSAPAVQTKSKKTLAKPNMKNIVVVEGVRIPFLLSGT
          MTTILTSTFRNLSTTSKWALRSSIRPLSCSSQLHSAPAVQTKSKKTLAKPNMKNIVVVEGVRIPFLLSGT
Retrocopy MTTILTSTFRNLSTTSKWALRSSIRPLSCSSQLHSAPAVQTKSKKTLAKPNMKNIVVVEGVRIPFLLSGT

Parental  SYKDLMPHDLARAALSGLLHRTNIPKDVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMACI
          SYKDLMPHDLARAALSGLLHRTNIPKDVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMACI
Retrocopy SYKDLMPHDLARAALSGLLHRTNIPKDVVDYIIFGTVIQEVKTSNVAREAALGAGFSDKTPAHTVTMACI

Parental  SSNQAMTTAVGLIASGQCDVVVAGGVELMSDVPIRHSRNMRKMMLDLNKAKTLGQRLSLLSKFRLNFLSP
          SSNQAMTTAVGLIASGQCDVVVAGGVELMSDVPIRHSRNMRKMMLDLNKAKTLGQRLSLLSKFRLNFLSP
Retrocopy SSNQAMTTAVGLIASGQCDVVVAGGVELMSDVPIRHSRNMRKMMLDLNKAKTLGQRLSLLSKFRLNFLSP

Parental  ELPAVAEFSTNETMGHSADRLAAAFAVSRMEQDEYALRSHSLAKKAQDEGHLSDIVPFKVPGKDTVTKDN
          ELPAVAEFSTNETMGHSADRLAAAFAVSRMEQDEYAL.SHSLAKKAQDEGHLSDIVPFKVPGKDTVTKDN
Retrocopy ELPAVAEFSTNETMGHSADRLAAAFAVSRMEQDEYALHSHSLAKKAQDEGHLSDIVPFKVPGKDTVTKDN

Parental  GIRPSSLEQMAKLKPAFIKPYGTVTAANSSFLTDGASAMLIMSEDRALAMGYKPKAYLRDFIYVSQDPKD
          GIRPSSLEQMAKLKPAFIKPYGTVTAANSSFLTDGASAMLIMSEDRALAMGYKPKAYLRDFIYVSQDPKD
Retrocopy GIRPSSLEQMAKLKPAFIKPYGTVTAANSSFLTDGASAMLIMSEDRALAMGYKPKAYLRDFIYVSQDPKD

Parental  QLLLGPTYATPKVLEKAGLTMNDIDAFEFHEAFSGQILANFKAMDSDWFAQNYMGRKTKVGSPPLEKFNI
          QLLLGPTYATPKVLEKAGLTMNDIDAFEFHEAFSGQILANFKAMDSDWFAQNYMGRKTKVGSPPLEKFNI
Retrocopy QLLLGPTYATPKVLEKAGLTMNDIDAFEFHEAFSGQILANFKAMDSDWFAQNYMGRKTKVGSPPLEKFNI

Parental  WGGSLSLGHPFGATGCRLVMAAANRLRKDGGQYALVAACAAGGQGHAMIVEAYPK
          WGGSLSLGHPFGATGCRLVMAAANRLRKDGGQYALVAACAAGGQGHAMIVEAYPK
Retrocopy WGGSLSLGHPFGATGCRLVMAAANRLRKDGGQYALVAACAAGGQGHAMIVEAYPK

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	0.42 RPM	18.41 RPM
SRP007412_cerebellum	0.26 RPM	15.37 RPM
SRP007412_heart	4.79 RPM	370.36 RPM
SRP007412_kidney	1.67 RPM	132.90 RPM
SRP007412_liver	0.38 RPM	43.61 RPM
SRP007412_testis	0.14 RPM	37.14 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1961 was not detected

EST

No EST(s) were mapped for retro_mmus_1961 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_78532	458 libraries	431 libraries	156 libraries	17 libraries	10 libraries

The graphical summary, for retro_mmus_1961 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_1961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1961 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002288	1 retrocopy	retro_amel_1473,
Canis familiaris	ENSCAFG00000029395	1 retrocopy	retro_cfam_2114,
Choloepus hoffmanni	ENSCHOG00000010050	3 retrocopies	retro_chof_122, retro_chof_1869, retro_chof_911,
Homo sapiens	ENSG00000138029	1 retrocopy	retro_hsap_4778,
Gorilla gorilla	ENSGGOG00000025829	1 retrocopy	retro_ggor_2976,
Microcebus murinus	ENSMICG00000006750	1 retrocopy	retro_mmur_1315,
Mus musculus	ENSMUSG00000059447	2 retrocopies	retro_mmus_1427, retro_mmus_1961 ,
Otolemur garnettii	ENSOGAG00000005444	1 retrocopy	retro_ogar_167,
Pongo abelii	ENSPPYG00000012582	1 retrocopy	retro_pabe_3718,
Pan troglodytes	ENSPTRG00000011733	1 retrocopy	retro_ptro_3180,
Tarsius syrichta	ENSTSYG00000003570	2 retrocopies	retro_tsyr_1316, retro_tsyr_1951,