RetrogeneDB ID: retro_mmus_62

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:82495418..82496537(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094374
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_62
ATGGCATACTCGGCAAACACAAACACCGTGCCTAAATTGTACAGATCTGTGATTGAAGATGTTATTAATGACGTACGAGA
CATTTTTCTGAATGATGGGGTGGATGAACAGGTCCTGACGGAACTAAAAGCTTTGTGGGAGAAAAACCTACTGCAGTCTA
GGGCAGTAGATGGATTTCGTTCAGAAGAACAGCAGCTTTTGTTGCAAGTTCAGCAGCAGCAGCAGCAACAGCATTACCAC
CACCAGCACCAGCAAGCACAACTTCAGCAAACGGTACCTCAGCAAGCACAGACCCAGCAGGTCCTTATTCCTGCATCCCA
GCAAGCTACAGCACCACAAGTTATTGTTCCTGATTCTAAGCTGCTACAACATATGAATGCATCAAGTATTCCGAGTGCTG
CTGCTACAGCTGCTACCTTGGCGCTCCCTGCAGGAGTGACTCCTGTTCAGCTACTAACAAATTCAAGCCAGCTGCTTCAG
GTGGTCAGAGCAGCCAATGGTGCCCAGTATATCTTGCAGCCTCAGCAGTCGGTTGTTCTACAACAAGTTATACCACAAAT
GCAGCCTGGTGGAGTCCAAGTGCCTGTTATCCAGCAGGTCCTAGCCCCACTTCCTGGAAGGATGTCACCACAGATGGGTG
TCATCATCCAGCCACAGCAAATCTTATTTCCAGGAAATAAGACTCAGGTCATTCCTACAACAGTGGCAGCACCCGCCCCG
GCACAAGCGCCGATGCCTGCAGCCGGACAGCAGCAGCCACAGGCCCAGCCTGCCCAACAGCAAGCTCCGCTGGTGCTGCA
AGTTGATGGAACAGGGGATACATCTTCTGAGGAAGATGAAGATGAAGATGAAGAAGAAGACTATGATGATGAGGAGGAAG
AAGATAAAGAGAAAGATGGAGCTGAAGATGGGCAGGTGGAAGAAGAGCCCCTCAACAGTGACGATGACTTAAGTGACGAG
GAAGGGCAGGAACCCTTTGACACAGAAAATGTTGTTGTCTGCCAGTATGATAAGATACACAGAAGTAAAAATAAATGGAA
ATTTCATCTCAAGGATGGCGTTATGAATCTTAACGGAAGAGATTATATATTTTCCAAAGCCTTGGAGATGCAGAGTGGT

Alignment

ORF - retro_mmus_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.6 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANSANTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAVDGFHSEEQQLLLQV
          MA.SANTNTVPKLYRSVIEDVINDVRDIFL.DGVDEQVL.ELK.LWE..L.QSRAVDGF.SE..Q.LL..
Retrocopy MAYSANTNTVPKLYRSVIEDVINDVRDIFLNDGVDEQVLTELKALWEKNLLQSRAVDGFRSE-EQQLLLQ

Parental  QQQHQPQQQQHHHHHHQHQQAQPQQTVPQQAQTQQVLIPASQQATAPQVIVPDSKLLQHMNASSITSAAA
          .Q....QQQQ..H.HHQHQQAQ.QQTVPQQAQTQQVLIPASQQATAPQVIVPDSKLLQHMNASSI.SAAA
Retrocopy VQ----QQQQQQHYHHQHQQAQLQQTVPQQAQTQQVLIPASQQATAPQVIVPDSKLLQHMNASSIPSAAA

Parental  TAATLALPAGVTPVQQLLTNSGQLLQVVRAANGAQYILQPQQSVVLQQQVIPQMQPGGVQAPVIQQVLAP
          TAATLALPAGVTPVQ.LLTNS.QLLQVVRAANGAQYILQPQQSVVLQQ.VIPQMQPGGVQ.PVIQQVLAP
Retrocopy TAATLALPAGVTPVQ-LLTNSSQLLQVVRAANGAQYILQPQQSVVLQQ-VIPQMQPGGVQVPVIQQVLAP

Parental  LPGGISPQTGVIIQPQQILFTGNKTQVIPTTVAAPAPAQAPMPAAGQQQPQAQPAQQQAPLVLQVDGTGD
          LPG..SPQ.GVIIQPQQILF.GNKTQVIPTTVAAPAPAQAPMPAAGQQQPQAQPAQQQAPLVLQVDGTGD
Retrocopy LPGRMSPQMGVIIQPQQILFPGNKTQVIPTTVAAPAPAQAPMPAAGQQQPQAQPAQQQAPLVLQVDGTGD

Parental  TSSEEDEDE--EEDYDDDEEEDKEKDGAEDGQVEEEPLNSEDDVSDEEGQELFDTENVVVCQYDKIHRSK
          TSSEEDEDE..EEDYDD.EEEDKEKDGAEDGQVEEEPLNS.DD.SDEEGQE.FDTENVVVCQYDKIHRSK
Retrocopy TSSEEDEDEDEEEDYDDEEEEDKEKDGAEDGQVEEEPLNSDDDLSDEEGQEPFDTENVVVCQYDKIHRSK

Parental  NKWKFHLKDGIMNLNGRDYIFSKAI
          NKWKFHLKDG.MNLNGRDYIFSKA.
Retrocopy NKWKFHLKDGVMNLNGRDYIFSKAL

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	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	0.03 RPM	19.03 RPM
SRP007412_testis	0.00 RPM	42.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_62 was not detected

EST

No EST(s) were mapped for retro_mmus_62 retrocopy.

TSS

No TSS is located nearby retro_mmus_62 retrocopy 5' end.

Lab

retro_mmus_62 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_62 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,