RetrogeneDB ID: retro_mmus_2251

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:49381333..49382745(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2af2
• Ensembl ID: ENSMUSG00000030435
• Aliases: U2af2, 65kDa
• Description: U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2 [Source:MGI Symbol;Acc:MGI:98886]

Sequence

>retro_mmus_2251
ATGTCGGACTTCGAGTTCAAGCGGCAGCTCAATGAGAATAAACAAGAACGGGACAAGGAGAATCAGCACAGGAAGCGTAG
TCACAGTCGCTCTTGAAGCGAGATCTAAAGCGCAGGAGCAGGAGCCGAGAGCGGCGCAACCTGGAACAGCGCAGTGCCTC
TCAGGGATAGGAGAGATGAAGCAAACCTTTGACCAGAGGCGCTAAAGAGGAGCACGGTGGATTGATTCGTTCTCCCCGCC
ATGAGAAGAAGAAGAAGGTGCATAAATACTGGGAAGTACCACCGCCTGGCTTTGAGCACATCACCTCAATGCAGTACAAG
GCCATGGAAGCTGCGGGTCAGATTCCAGCCACTGCCCTTCTCCCGACCATGACTCCTGATGGTCTGGCTGTGACCCCCAA
CGCCAGTGCCTGTGGTTGGGAGCCAGATGACAAGACAGGCCAGACGTCTCTATGTGGGCAACATCCCTTTTGGCATTACT
GAGGAGGCTATGATGGACTTCTTCAACGCCCAGATGTGCTTGGGGGGGGGGGTGACTCAGGCCCCTGGCAACCCAGTCTT
GGCTGTGCAGATAAATCAAGACAAGAATTTTGCCTTTTTGGAGTTCCGGTCAGTGGATGAGATGACCCAGGCCATGGCCT
TTGATGGCATCATCTTCCAGGGCCAGTCATTGAAGATCGAAGGCCTCATGACTATCAGCCATTGCCTGGCATGTCAGAGA
ACCCCTCTGTTTATGTGCCTGGAGTTGTATCCACTGTAGTCCCAGATTCTGCCCAAAAGCTGTTCATCGGGGGTTTGCCC
AATTACCTACATGATGACCAGTTAAAAGAGCTGCTGACATCCTTTGGGCCTCTCAAGGCCTTCAACTTGGTTAAGGATAG
TGCCACAGGGCTCTCCAAGGGCTATGCCTTCAGTGAGTATGTGGACATCAACGTCACAGATCAGGCCATTGCGGGGCTGA
ATGGGATGCAGCTAGGGGACAAGAAGCTGCTTGTCCAGAGGGCGAGTGTGGGAGCCAAGAATGCCACGCTGAGCACCATC
AATCAGACACCTGTGACCCTTCAAGTGCCCGGCCTAATGAGCTCTCAGGTGCAGATGGGCGGTCACCCAACTGAGGTCCT
GTGCCTCATGAACATGGTGCTGCCTGAGGAGCTGCTGGACGATGAGGAGTATGAGGAGATTGTAGAGGACGTACGAGACG
AGTGCAGCAAGTATGGGTTGGTCAAATCCATTGAAATTCCCCGCCCTGTGGACTGCGTGGAGGTGCCTGGCTGTGGAAAG
ATCTTCGTGGAGTTCACCTCTGTGTTTGACTGTCAGAAAGCCCTGCAGGGTCTAACCGGTCGCAAGTTCGCCAACAGAGT
GGTGGTCACAAAATACTGTGACCCTGATTCTTACCACCGTCGGGACTTCTGG

Alignment

ORF - retro_mmus_2251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDFDEFERQLNENKQERDKENRHRKRSHSRSRS-RDRKRRSRSRDRRNRDQRSASRDRRRRSKPLTRGA
          MSDF.EF.RQLNENKQERDKEN.HRKRSHSRS.S.RD.KRRSRSR.RRN..QRSAS....R.SKPLTRGA
Retrocopy MSDF-EFKRQLNENKQERDKENQHRKRSHSRS*S<RDLKRRSRSRERRNLEQRSASQG*ER*SKPLTRGA

Parental  KEEHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTP-TPVP
          KEEHGGLIRSPRHEKKKKV.KYW.VPPPGFEHIT.MQYKAM.AAGQIPATALLPTMTPDGLAVTP.TPVP
Retrocopy KEEHGGLIRSPRHEKKKKVHKYWEVPPPGFEHITSMQYKAMEAAGQIPATALLPTMTPDGLAVTP>TPVP

Parental  VVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQM-RLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE
          VVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQM......TQAPGNPVLAVQINQDKNFAFLEFRSVDE
Retrocopy VVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMCXXXXXTQAPGNPVLAVQINQDKNFAFLEFRSVDE

Parental  TTQAMAFDGIIFQGQSLKI-RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVK
          .TQAMAFDGIIFQGQSLKI.RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSA.KLFIGGLPNYL.DDQ.K
Retrocopy MTQAMAFDGIIFQGQSLKI<RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAQKLFIGGLPNYLHDDQLK

Parental  ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATLVS
          ELLTSFGPLKAFNLVKDSATGLSKGYAF.EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATL..
Retrocopy ELLTSFGPLKAFNLVKDSATGLSKGYAFSEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATL--

Parental  LPSTINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE
          ..STINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE
Retrocopy --STINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE

Parental  IPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW
          IPRPVD.VEVPGCGKIFVEFTSVFDCQKA.QGLTGRKFANRVVVTKYCDPDSYHRRDFW
Retrocopy IPRPVDCVEVPGCGKIFVEFTSVFDCQKALQGLTGRKFANRVVVTKYCDPDSYHRRDFW

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	0.12 RPM	72.96 RPM
SRP007412_cerebellum	0.00 RPM	76.86 RPM
SRP007412_heart	0.16 RPM	54.70 RPM
SRP007412_kidney	0.08 RPM	63.72 RPM
SRP007412_liver	0.05 RPM	43.15 RPM
SRP007412_testis	0.05 RPM	51.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2251 was not detected

EST

No EST(s) were mapped for retro_mmus_2251 retrocopy.

TSS

No TSS is located nearby retro_mmus_2251 retrocopy 5' end.

Lab

retro_mmus_2251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2251 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
Loxodonta africana	ENSLAFG00000018056	1 retrocopy	retro_lafr_94,
Myotis lucifugus	ENSMLUG00000011051	2 retrocopies	retro_mluc_406, retro_mluc_797,
Macaca mulatta	ENSMMUG00000004810	1 retrocopy	retro_mmul_30,
Mus musculus	ENSMUSG00000030435	3 retrocopies	retro_mmus_2251 , retro_mmus_3663, retro_mmus_991,
Otolemur garnettii	ENSOGAG00000007206	1 retrocopy	retro_ogar_3304,