RetrogeneDB ID: retro_mmus_760

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:8805954..8806725(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081539
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gtf2a1
• Ensembl ID: ENSMUSG00000020962
• Aliases: Gtf2a1, 6330549H03Rik, AA536742, AA959775, AW060250, TfIIAa/b, Tfiia1
• Description: general transcription factor II A, 1 [Source:MGI Symbol;Acc:MGI:1933277]

Sequence

>retro_mmus_760
GCTACAGCGCCACCACTTATTGTTACCGATTCTAAGTTCATACAACATATGAATGCATCAAGTATTCTGAGTGCTGTTGC
TACAGCTGCTACCTTGGCACTCCCTGCAGACGTGACTCCTGTCAACAGATACTAACAAATTCAGGCCAGCTGTTTCAGGT
GGTCAGAGCAGCCAATGGTGCTCAGTTATCTTTCAGCCTCAGCAGTCAGTTGTTCTACAAGTTATACCACAAATGCAACC
TGATGGAGTACAAGCGCCTGTTATCCAGCAGGTCCTAGCCCTACTTCCTGGAAGGATGTCATCACAGACAGGTGTCATCA
TCCAGCCACAGCAAATCTTATTTACAGGAAATAAGACTCAGGTCATCCCTACAACCATGGCAGCACAAGCACAGATGACT
GCAGCTGGACAGCAGCAGCCACCAGCCCAGCCCGTTCAACAGCAAGCTCCATTGGTGCTGCAAGGTGACAGAAAGGGGGA
TACATCTGAGGAAGATGGAGATGAAGAAGAAGGCTATGATGAGGAGGAAGAGGAATAGAAAGAGAAAGATGGAGCTGAAG
ATGGGCAGGTGGAAGAAGAGCCCCTCAACAGTGAAGATGATGTAAGTGACGAGGAAGGGCAGGAACTCTTTGACACAGAA
AATGTTGTTGTATGCCAGTATGATAAGATACACAGAAGTAAAAATAAATGGAAATTTCATCTCAAGGATGACATTATGAT
CTTAATGGAAGAGATTATATATTTTCCAAAGCCATTGAAGATGCAGAGTGG

Alignment

ORF - retro_mmus_760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.96 %
• Parental protein coverage: 70.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ATAPQVIVPDSKLLQHMNASSITSAAATAATLALPAGVTPV-QQLLTNSGQLLQVVRAANGAQY-ILQPQ
          ATAP..IV.DSK..QHMNASSI.SA.ATAATLALPA.VTPV.QQ.LTNSGQL.QVVRAANGAQ..I.QPQ
Retrocopy ATAPPLIVTDSKFIQHMNASSILSAVATAATLALPADVTPV<QQILTNSGQLFQVVRAANGAQL<IFQPQ

Parental  QSVVLQQQVIPQMQPGGVQAPVIQQVLAPLPGGISPQTGVIIQPQQILFTGNKTQVIPTTVAAPAPAQAP
          QSVVLQ..VIPQMQP.GVQAPVIQQVLA.LPG..S.QTGVIIQPQQILFTGNKTQVIPTT.A....AQA.
Retrocopy QSVVLQ--VIPQMQPDGVQAPVIQQVLALLPGRMSSQTGVIIQPQQILFTGNKTQVIPTTMA----AQAQ

Parental  MPAAGQQQPQAQPAQQQAPLVLQVDGTGDTSSEEDEDEEEDYDDDEEEDKEKDGAEDGQVEEEPLNSEDD
          M.AAGQQQP.AQP.QQQAPLVLQ.D..GDTS.EED.DEEE.YD..EEE.KEKDGAEDGQVEEEPLNSEDD
Retrocopy MTAAGQQQPPAQPVQQQAPLVLQGDRKGDTS-EEDGDEEEGYDEEEEE*KEKDGAEDGQVEEEPLNSEDD

Parental  VSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIM-NLNGRDYIFSKAIGDAEW
          VSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKD.IM..LNGRDYIFSKAI.DAEW
Retrocopy VSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDDIM<DLNGRDYIFSKAIEDAEW

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	34.95 RPM
SRP007412_cerebellum	0.00 RPM	38.56 RPM
SRP007412_heart	0.00 RPM	19.02 RPM
SRP007412_kidney	0.04 RPM	30.40 RPM
SRP007412_liver	0.00 RPM	19.03 RPM
SRP007412_testis	0.82 RPM	42.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_760 was not detected

EST

No EST(s) were mapped for retro_mmus_760 retrocopy.

TSS

No TSS is located nearby retro_mmus_760 retrocopy 5' end.

Lab

retro_mmus_760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_760 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000017256	1 retrocopy	retro_mluc_176,
Mus musculus	ENSMUSG00000020962	2 retrocopies	retro_mmus_62, retro_mmus_760 ,