RetrogeneDB ID: retro_mmus_2283

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:103644835..103646023(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000087119
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atg4a
• Ensembl ID: ENSMUSG00000079418
• Aliases: Atg4a, AI627006, AV169859, Apg4a, Atg4al, Autl2
• Description: autophagy related 4A, cysteine peptidase [Source:MGI Symbol;Acc:MGI:2147903]

Sequence

>retro_mmus_2283
ATGGAGTCAGTTATGTCCAAGTATGAAAACCAGATTCTTATTTTCCCTGACTACCTGGAAGAATTCCCGGATACAGATGA
GCTGGTATGGATTCTGGGGAAGCAGCACCCCTTTAAGACAGAAAAATCTAAGCTGTTGTCTGATATAAGTGCTCGCCTAT
GGTTTACATACAGAAGGAAATTTTCCCCGATTGGGGGAACAGGCCCTTCATCTGATGCTGGATGGGGATGTATGCTGCGT
TGTGGGCAGATGATGCTGGCTCAAGCCCTCATCTGCAGACACTTGGGAAGGGATTGGAACTGGGAGAGACAAAAAGAACA
ACCCAAAGAATACCAAAGGATACTGCAGTGTTTCCTAGATAGAAAAGACTGTTGCTATTCAATCCATCAGATGGCACAAA
TGGGTGTAGGAGAAGGGAAATCAATTGGCGAATGGTTTGGACCAAACACAGTTGCACAGGTGATAAAAAAACTCACTTTA
TTTGATGAATGGAATTCCTTGGCTGTTTATGTTTCCATGGATAACACAGTGGTCATTGAAGATATCAAGAAAATGTGCTG
TGTTCTTCCTGTGGGTGCTGCTGACCCAGCTGGTGATTTTCTGACTGTATCCAATCAGAGTAGAGACACCTCTGTCCCGT
GCTCAGCCTGGAAACCCCTGCTGCTCATTGTGCCCCTTCGCTTGGGCATAAACCAAATCAATCCTGTGTATGTTGAAGCA
TTCAAAGAGTGTTTTAAGATGCCACAGTCTTTAGGGGCTTTAGGAGGAAAGCCAAATAACGCCTATTATTTCATAGGATT
CTTAGGAGATGAGCTCATTTTTTTGGACCCTCACACAACCCAGACTTTTGTTGACATTGAAGAGAGTGGACTAGTAGACG
ACCAGACTTTTCATTGCCTGCAGTCTCCACAGCGGATGAGTATCCTGAACTTGGATCCTTCTGTGGCCTTGGGATTTTTC
TGCAAAGAAGAGAAAGACTTTGATAATTGGTGTAGCCTTGTTCAGAAGGAAATTCTAAAGGAGAATTTGAGGATGTTTGA
ATTGGTTCAGAAGCACCCATCACACTGGCCTCCCTTTGTACCTCCAGCCAAGCCAGAAGTGACAACCACAGGGGCAGAAT
TCATAGAGTCGACTGAACAACTGGAGGACTTTGAGCTGGAGGAAGATTTTGAAATTCTGAGTGTAGGC

Alignment

ORF - retro_mmus_2283 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESVMSKYENQILIFPDYLEEFPDTDELVWILGKQHPLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPS
          MESVMSKYENQILIFPDYLEEFPDTDELVWILGKQHP.KTEKSKLLSDISARLWFTYRRKFSPIGGTGPS
Retrocopy MESVMSKYENQILIFPDYLEEFPDTDELVWILGKQHPFKTEKSKLLSDISARLWFTYRRKFSPIGGTGPS

Parental  SDAGWGCMLRCGQMMLAQALICRHLGRDWNWERQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGK
          SDAGWGCMLRCGQMMLAQALICRHLGRDWNWERQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGK
Retrocopy SDAGWGCMLRCGQMMLAQALICRHLGRDWNWERQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGK

Parental  SIGEWFGPNTVAQVIKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCCVLPVGAADPAGDFLTASNQSRDT
          SIGEWFGPNTVAQVIKKL.LFDEWNSLAVYVSMDNTVVIEDIKKMCCVLPVGAADPAGDFLT.SNQSRDT
Retrocopy SIGEWFGPNTVAQVIKKLTLFDEWNSLAVYVSMDNTVVIEDIKKMCCVLPVGAADPAGDFLTVSNQSRDT

Parental  SVPCSAWKPLLLIVPLRLGINQINPVYVEAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTT
          SVPCSAWKPLLLIVPLRLGINQINPVYVEAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTT
Retrocopy SVPCSAWKPLLLIVPLRLGINQINPVYVEAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTT

Parental  QTFVDIEESGLVDDQTFHCLQSPQRMSILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQ
          QTFVDIEESGLVDDQTFHCLQSPQRMSILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQ
Retrocopy QTFVDIEESGLVDDQTFHCLQSPQRMSILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQ

Parental  KHPSHWPPFVPPAKPEVTTTGAEFIESTEQLEDFELEEDFEILSVG
          KHPSHWPPFVPPAKPEVTTTGAEFIESTEQLEDFELEEDFEILSVG
Retrocopy KHPSHWPPFVPPAKPEVTTTGAEFIESTEQLEDFELEEDFEILSVG

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	0.02 RPM	3.32 RPM
SRP007412_cerebellum	0.00 RPM	3.08 RPM
SRP007412_heart	0.03 RPM	6.10 RPM
SRP007412_kidney	0.15 RPM	7.76 RPM
SRP007412_liver	0.14 RPM	3.80 RPM
SRP007412_testis	0.00 RPM	0.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2283 was not detected

EST

No EST(s) were mapped for retro_mmus_2283 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_90649	100 libraries	106 libraries	656 libraries	177 libraries	33 libraries

The graphical summary, for retro_mmus_2283 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_2283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2283 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000002971	1 retrocopy	retro_ggor_2935,
Mus musculus	ENSMUSG00000026280	1 retrocopy	retro_mmus_3387,
Mus musculus	ENSMUSG00000079418	1 retrocopy	retro_mmus_2283 ,
Nomascus leucogenys	ENSNLEG00000014016	1 retrocopy	retro_nleu_1993,
Pongo abelii	ENSPPYG00000020619	1 retrocopy	retro_pabe_3666,
Pan troglodytes	ENSPTRG00000022170	1 retrocopy	retro_ptro_3139,