RetrogeneDB ID: retro_mmus_1406

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:74080236..74081511(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000075609
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sf3b4
• Ensembl ID: ENSMUSG00000068856
• Aliases: Sf3b4, 49kDa, SF3b49, SF3b50, Sap49
• Description: splicing factor 3b, subunit 4 [Source:MGI Symbol;Acc:MGI:109580]

Sequence

>retro_mmus_1406
ATGGCTGCCGGACCGATCTCCGAACGGAATCAGGATGCCACGGTGTACGTGGGCGGTCTGGACGAGAAAGTGAGTGAGCC
GCTGCTGTGGGAGCTCTTTCTCCAGGCAGGGCCAGTGGTCAACACCCACATGCCAAAGGACAGAGTCACTGGCCAGCACC
AGGGCTATGGCTTTGTTGAATTCCTGAGCGAGGAAGATGCCGACTATGCCATTAAGATTATGAACATGATCAAACTCTAT
GGAAAGCCAATACGGGTGAACAAGGCCTCAGCTCACAACAAAAACCTGGATGTGGGAGCCAACATTTTCATTGGAAATCT
GGACCCAGAAATTGATGAAAAGCTGCTTTACGATACTTTCAGAGCCTTTGGAGTCATCCTACAGACCCCCAAGATCATGT
GGGACCCTGACACAGGCAACTCCAAGGGTTACTCCTTCATTAATTTTGCCTCCTTCGATGCTTCGGATGCAGCAATTGAG
GCCATGAACGGGCAGTACCTGTGTAACCGTCCTATCACTGTGTCTTATGCCTTCAAGAAGGACTCTAAGGGTGAACGCCA
TGGCTCAGCAGCTGAAAGACTCCTGGCAGCCCAGAACCCGCTGTCCCAGGCTGACCGCCCTCATCAGCTGTTTGCCGATG
CACCCCCTCCGCCCTCTGCCCCCAATCCCGTGGTTTCATCCCTGGGTTCTGGGCTTCCTCCACCAGGCATGCCGCCTCCT
GGCTCTTTTCCACCTCCAGTGCCACCTCCTGGGGCCCTCCCTCCTGGGATTCCCCCAGCCATGCCCCCACCACCTATGCC
ACCTGGGGCTGGAGGACATGGCCCCCCAGCAGCAGGGACTCCAGGGGCTGGACATCCCGGTCACGGACACTCACATCCTC
ACCCGTTCCCACCAGGTGGGATGCCCCATCCAGGGATGTCCCAGATGCAGCTGGCCCACCATGGCCCCCATGGCCTAGGA
CACCCCCATGCTGGGCCTCCGGGCTCTGGGGGGCAGCCACCACCTCGGCCACCTCCTGGAATGCCTCATCCTGGACCTCC
TCCAATGGGCATGCCCCCCCCCCGAGGGCCTCCTTTTGGATCTCCCATGGGTCACCCAGATCCCATGCCTCCACACGGCA
TGCGTGGGCCTCCTCCATTGATGCCCCCTCATGGATACACGGGTCCTCCAAGACCCCCTCCCTATGGCTACCAGCGGGGG
CCCCTCCCGCCACCCAGACCCACTCCACGGCCCCCAGTTCCACCTCGTGGTCCTCTTCGGGGCCCACTTCCTCAG

Alignment

ORF - retro_mmus_1406 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
          MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
Retrocopy MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA

Parental  IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGN
          IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTF.AFGVILQTPKIM.DPDTGN
Retrocopy IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFRAFGVILQTPKIMWDPDTGN

Parental  SKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQL
          SKGY.FINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQL
Retrocopy SKGYSFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQL

Parental  FADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPAAGT
          FADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPAAGT
Retrocopy FADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPAAGT

Parental  PGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMG
          PGAGHPGHGHSHPHPFPPGGMPHPGMSQMQ.........GHPHAGPPGSGGQPPPRPPPGMPHPGPPPMG
Retrocopy PGAGHPGHGHSHPHPFPPGGMPHPGMSQMQXXXXXXXXXGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMG

Parental  M-PPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLR
          M....GPPFGSPMGHP.PMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLR
Retrocopy MXXXXGPPFGSPMGHPDPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLPPPRPTPRPPVPPRGPLR

Parental  GPLPQ
          GPLPQ
Retrocopy GPLPQ

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	0.05 RPM	10.42 RPM
SRP007412_cerebellum	0.00 RPM	9.73 RPM
SRP007412_heart	0.06 RPM	3.67 RPM
SRP007412_kidney	0.00 RPM	7.20 RPM
SRP007412_liver	0.03 RPM	4.10 RPM
SRP007412_testis	0.05 RPM	28.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1406 was not detected

EST

No EST(s) were mapped for retro_mmus_1406 retrocopy.

TSS

No TSS is located nearby retro_mmus_1406 retrocopy 5' end.

Lab

retro_mmus_1406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1406 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Felis catus	ENSFCAG00000010106	1 retrocopy	retro_fcat_1607,
Mus musculus	ENSMUSG00000042396	1 retrocopy	retro_mmus_2436,
Mus musculus	ENSMUSG00000068856	1 retrocopy	retro_mmus_1406 ,
Otolemur garnettii	ENSOGAG00000006265	3 retrocopies	retro_ogar_2227, retro_ogar_2388, retro_ogar_2804,