RetrogeneDB ID: retro_mmus_889

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:88334623..88335475(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snrpa
• Ensembl ID: ENSMUSG00000061479
• Aliases: Snrpa, C430021M15Rik, Rnu1a-1, Rnu1a1, U1-A, U1A
• Description: small nuclear ribonucleoprotein polypeptide A [Source:MGI Symbol;Acc:MGI:1855690]

Sequence

>retro_mmus_889
ACCATGGCCACCATGCCAGTTCCTGAGACCCGTTTAAACCACACTATTTATATCAACAATCTCAATGAGAAGATCAAGAA
GGATGAGCTCAAGAAGTCCCTGTATGCCTTCTTCTCCCAGTTTGGCCAGATCCTGGATATCCTGGTGTCTCGGAGCCTGA
AGATGAGGAGCCAGGCCTTCGTCATCTTCAAGGAGGTCACCAGCGCCACCAATGCCCTGCGCTCCATGCAGGGCTTCCCT
TTCTATGATAAGCCCATGCGCATCCAGTACGCAAAGACTGACTCGGACATCATTGCCAAGATGACGGGCACCTTTGTGGA
GAGAGATCGCAAAGGAGAGAAGAGGAAGCCCAAGAGTCAGGAGACACCTGCTGCCAAAAAGGCTGTTCAGGGTGGGGCAG
CTGCCCCTGTGGTGGGTGCTGTCCAGCCTGTACCGGGCATGCCACCAATGCCTCAGGCACCCCGCATCATGCACCGCATG
CCAGGACAGCCTCCCTACATGCCATACCTGGCATGATCCCGCCAACAATCCTCGCTCCTGGCCAGATCCCCCCTGGGGCC
ATGCCCCCACAGCAGCTCATGCCTGGGCAGATGCCGCCTGCCCAGCCTCTCTCCGAGAATCCACGCAATCATCCTGTTCT
TCACCAACCAGCCTGAGGAGACCAACGAGCTCATGCTCTCCATGTTTTTTACCCAGTTCCCTGTCTTCAAGGAGGTGCAT
CTGGTCCCTGGGCGCCATGACATCGCCTTCGTGGAGTTTGACAATGAAGTGCAAGCTGGGGCAGCAATAGATGCCCTGCA
AGGCTTTAAGATCACACAAAACAATGCTATGAAGATCTCTTTTGCCAAGAAG

Alignment

ORF - retro_mmus_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.29 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TIATMPVPETRANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSAT
          T.ATMPVPETR.NHTIYINNLNEKIKKDELKKSLYA.FSQFGQILDILVSR..KMR.QAFVIFKEVTSAT
Retrocopy TMATMPVPETRLNHTIYINNLNEKIKKDELKKSLYAFFSQFGQILDILVSRSLKMRSQAFVIFKEVTSAT

Parental  NALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYVERDRKREKRKPKSQETPAAKKAVQGGAAAPVVGA
          NALRSMQGFPFYDKPMRIQYAKTDSDIIAKM.GT.VERDRK.EKRKPKSQETPAAKKAVQGGAAAPVVGA
Retrocopy NALRSMQGFPFYDKPMRIQYAKTDSDIIAKMTGTFVERDRKGEKRKPKSQETPAAKKAVQGGAAAPVVGA

Parental  VQPVPGMPPMPQAPRIMHHMPGQPPYMP-PPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPP
          VQPVPGMPPMPQAPRIMH.MPGQPPYMP..PGMIPP..LAPGQIPPGAMPPQQLMPGQMPPAQPLSENP.
Retrocopy VQPVPGMPPMPQAPRIMHRMPGQPPYMP<IPGMIPPTILAPGQIPPGAMPPQQLMPGQMPPAQPLSENPR

Parental  NH-ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAM
          NH...F.TN.PEETNELMLSM.F.QFP.FKEV.LVPGRHDIAFVEFDNEVQAGAA.DALQGFKITQNNAM
Retrocopy NH>LFF-TNQPEETNELMLSMFFTQFPVFKEVHLVPGRHDIAFVEFDNEVQAGAAIDALQGFKITQNNAM

Parental  KISFAKK
          KISFAKK
Retrocopy KISFAKK

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	23.99 RPM
SRP007412_cerebellum	0.00 RPM	18.58 RPM
SRP007412_heart	0.00 RPM	15.44 RPM
SRP007412_kidney	0.00 RPM	13.98 RPM
SRP007412_liver	0.00 RPM	10.16 RPM
SRP007412_testis	0.00 RPM	29.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_889 was not detected

EST

No EST(s) were mapped for retro_mmus_889 retrocopy.

TSS

No TSS is located nearby retro_mmus_889 retrocopy 5' end.

Lab

retro_mmus_889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_889 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005091	1 retrocopy	retro_cfam_1114,
Callithrix jacchus	ENSCJAG00000014865	1 retrocopy	retro_cjac_287,
Cavia porcellus	ENSCPOG00000010875	1 retrocopy	retro_cpor_663,
Myotis lucifugus	ENSMLUG00000000219	1 retrocopy	retro_mluc_1517,
Monodelphis domestica	ENSMODG00000007912	1 retrocopy	retro_mdom_447,
Mustela putorius furo	ENSMPUG00000017681	1 retrocopy	retro_mputfur_593,
Mus musculus	ENSMUSG00000008333	4 retrocopies	retro_mmus_1496, retro_mmus_1497, retro_mmus_2378, retro_mmus_3325,
Mus musculus	ENSMUSG00000061479	6 retrocopies	retro_mmus_275, retro_mmus_3374, retro_mmus_469, retro_mmus_888, retro_mmus_889 , retro_mmus_958,
Otolemur garnettii	ENSOGAG00000002864	1 retrocopy	retro_ogar_2046,
Pteropus vampyrus	ENSPVAG00000001494	1 retrocopy	retro_pvam_832,