RetrogeneDB ID: retro_mmus_3374

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:101448499..101449354(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000061486
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_3374
ACATCTCACACCATGGCAGTTCCCGAGACCCGTCCCAACCACACTATTTATATCAACAGTCTCAACGAGAAGATCAAGAA
AGATGAGCTCAAGAAGTCCCCGTATGCCATCTTCTCCCAGTTTGGCCAGATCCTGGATATCCTGGTGTCTCAGAGCCTGA
AGATGAGGGGCCAGTCCTTCGTCATCTTCAAGGAGGTCAGCAGCACCATCAACGCCCTGCGCTCCATGCAGGGCTTCCCC
TTCTACGGCAAGCCCATGCATATCCAGTACGCAAAGACTGACTCGGACATCATTGCCAAGATGAAGGGCACCTTTGTGGA
GAGAGATCGCAAACGAGAGAAGAGGAAGCCCAAGAGTCAGGAGAAACCTGCTGTCAAAAAAGGCTGTTCAGGGTGGGGCA
GTGCCCCCGTGGTGGGTGCTGTCCAGCCTGTACCGGGCATGCCACCGATGCCTCAGGCACCCCGTGTTATGCACCACATG
CCAGGACAGCCTCCCTACATGCGACCACCTGGCATGATCCTGCCACCAGGCCTCCCTCCTGGCCAGATCCCCTCTAGGGC
CATGCCCCCACAGCAGCTCATACCTGGGCAGATGCCGCATGCGCAGCCTCTCTCCGAGAATCCACCCAATCACATCCTGT
TCCTCACCAACCTGCCTGAGGAGACCAACGAGCTCATGCTCTCCATGCTTTTCACCCAGTTCCCTGGCTTCAAGGAGGTG
CGTCTGGTCCCTGGGCGCCATGACATCGACTTCGTGGAGTTTGACAATGAAGTGCAGGCTGGAGCAGCACGAGATGTCCT
GCAAGGCTTTAAGATCACACAGAACAATGCTATGAAGATCTCTTTTGCCAAGAAG

Alignment

ORF - retro_mmus_3374 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.72 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIATMPVPETRANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSAT
          T..TM.VPETR.NHTIYIN.LNEKIKKDELKKS.YAIFSQFGQILDILVS...KMRGQ.FVIFKEV.S..
Retrocopy TSHTMAVPETRPNHTIYINSLNEKIKKDELKKSPYAIFSQFGQILDILVSQSLKMRGQSFVIFKEVSSTI

Parental  NALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYVERDRKREKRKPKSQETPAAKKAVQGGAAAPVVGA
          NALRSMQGFPFY.KPM.IQYAKTDSDIIAKMKGT.VERDRKREKRKPKSQE.PA.KK...G...APVVGA
Retrocopy NALRSMQGFPFYGKPMHIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQEKPAVKKGCSGWGSAPVVGA

Parental  VQPVPGMPPMPQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPN
          VQPVPGMPPMPQAPR.MHHMPGQPPYM.PPGMI.PPGL.PGQIP..AMPPQQL.PGQMP.AQPLSENPPN
Retrocopy VQPVPGMPPMPQAPRVMHHMPGQPPYMRPPGMILPPGLPPGQIPSRAMPPQQLIPGQMPHAQPLSENPPN

Parental  HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI
          HILFLTNLPEETNELMLSMLF.QFPGFKEVRLVPGRHDI.FVEFDNEVQAGAARD.LQGFKITQNNAMKI
Retrocopy HILFLTNLPEETNELMLSMLFTQFPGFKEVRLVPGRHDIDFVEFDNEVQAGAARDVLQGFKITQNNAMKI

Parental  SFAKK
          SFAKK
Retrocopy SFAKK

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	23.99 RPM
SRP007412_cerebellum	0.04 RPM	18.58 RPM
SRP007412_heart	0.09 RPM	15.44 RPM
SRP007412_kidney	0.02 RPM	13.98 RPM
SRP007412_liver	0.00 RPM	10.16 RPM
SRP007412_testis	0.05 RPM	29.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3374 was not detected

EST

No EST(s) were mapped for retro_mmus_3374 retrocopy.

TSS

No TSS is located nearby retro_mmus_3374 retrocopy 5' end.

Lab

retro_mmus_3374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3374 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,