RetrogeneDB ID: retro_mmus_2650

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:44405957..44406555(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rab2a
• Ensembl ID: ENSMUSG00000047187
• Aliases: Rab2a, 9330148M11Rik, C80220, Rab2
• Description: RAB2A, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:1928750]

Sequence

>retro_mmus_2650
GACACAGGTGTTGGTAAATCGTGCTTATTGCTACAGTTTACAGACAAGAGGTTTCAGCCGGTGCATGACCTCACAATTGG
TGTAGAGTTTGGTGCTCAGATGATAAAGATTGATGGGAAAGAGATAAAACTCCAGATCTGGGATACAGCAGGGCAAGAGT
CCTTTTGTTCTATCACAAGGTCATATTACAGAGGTGCAGCGGGGGCTTTACTAGTGTATGATATTACAAGGAGAGACACT
TTCAACCACTTGACAACCTGGTTAGAAGATGCCCGTCAGCATTCCAATTCCAACATGGTCATCACGCTTATTGGAAATAA
AAGTGACTTAGAATCTAGGAGAGAAGAGAAAAGGGAAGAAGGTGAAGCTTTTGCACGAGAGCATGGACTTATCTTCATGG
AAACTTCTGCCAAGACGGCTTCTAATGTAGAGGAGGCATTTATTAACACAGCAAAAGAAATTTATGAAAAAAAGCTAAGA
AGGGGTCTTTGACATTAATAATGAGGCAAACGGCATTAAAATTAGCCCTCAGCACGCTGTTACCAACGCATCTCATGGAA
GCAACCAAGGCGGACCGCAGGCAGGGGGAGGCTGCTGT

Alignment

ORF - retro_mmus_2650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.5 %
• Parental protein coverage: 93.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGAL
          DTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGA.MI.IDGK.IKLQIWDTAGQESF.SITRSYYRGAAGAL
Retrocopy DTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGAQMIKIDGKEIKLQIWDTAGQESFCSITRSYYRGAAGAL

Parental  LVYDITRRDTFNHLTTWLEDARQHSNSNMVIMLIGNKSDLESRREVKKEEGEAFAREHGLIFMETSAKTA
          LVYDITRRDTFNHLTTWLEDARQHSNSNMVI.LIGNKSDLESRRE.K.EEGEAFAREHGLIFMETSAKTA
Retrocopy LVYDITRRDTFNHLTTWLEDARQHSNSNMVITLIGNKSDLESRREEKREEGEAFAREHGLIFMETSAKTA

Parental  SNVEEAFINTAKEIYEKIQ-EGVFDINNEANGIKIGPQHAATNASHGSNQGGQQAGGGCC
          SNVEEAFINTAKEIYEK...EGVFDINNEANGIKI.PQHA.TNASHGSNQGG.QAGGGCC
Retrocopy SNVEEAFINTAKEIYEKKL>EGVFDINNEANGIKISPQHAVTNASHGSNQGGPQAGGGCC

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	0.19 RPM	179.71 RPM
SRP007412_cerebellum	0.09 RPM	159.70 RPM
SRP007412_heart	0.12 RPM	106.34 RPM
SRP007412_kidney	0.15 RPM	119.08 RPM
SRP007412_liver	0.05 RPM	79.60 RPM
SRP007412_testis	0.32 RPM	63.17 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2650 was not detected

EST

No EST(s) were mapped for retro_mmus_2650 retrocopy.

TSS

No TSS is located nearby retro_mmus_2650 retrocopy 5' end.

Lab

retro_mmus_2650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2650 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007700	1 retrocopy	retro_eeur_496,
Echinops telfairi	ENSETEG00000010340	2 retrocopies	retro_etel_203, retro_etel_32,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Mus musculus	ENSMUSG00000047187	1 retrocopy	retro_mmus_2650 ,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846,