RetrogeneDB ID: retro_mmus_352

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:110600020..110600833(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ammecr1l
• Ensembl ID: ENSMUSG00000041915
• Aliases: Ammecr1l, 5430429D03Rik, AU022236, AU040755, AW111353, E230022H04Rik
• Description: AMME chromosomal region gene 1-like [Source:MGI Symbol;Acc:MGI:2442711]

Sequence

>retro_mmus_352
CAGTCTACAACTGTTCCTGGCTCAAGTTCAGGACCTCTTCAAAACCACCAGCATGTAGACAGCAGCAGTTGTATGGAAAA
TGTATCCAACTTAACTCTGGTACCTGGAAACTCTCCTATGAATCCTCCTCTGCAGCCCTGATCCCTCTCCCCTGACCCAA
TGGAACTAACTGCCAATACCTCTAAGAACCTGGTGGTGAGTGCAGAGATGTGCTGCTACTGCTTTGATGTGCTCTACTGT
CACCTCTATGGCTTTCCACAGCCACGACTTCCTAGATTCAGCAGTGACCCTTATCCTCTCTTTGTGACCTGGAAGACAGG
ACGAGACAAGTGGCTTTGTGGCTGCATTGGGACCTTCTCAGCCATGAATCTTCATTCAGGACTCAGCGAATACTCATTAA
TCAGTGTACTTAAGGACAGCCAGTTCCTGCCACTGACCTGAGAGGAGCTGCCCAAACTTGTCTGTTCTGTCTCCCTCCTT
ACTAACTTTGAAGATGCAAGTGATTACATGAATTGGGAGATAGGGGTCCATGGGAAACAGATTGAATTCATCAAGGAAAA
AGGCATCAAACACACAACCACATATTTACCTGAGGTTGCTAAGGAATACGATTGGGATCAGATCCAGACTCTAGACTCCT
TGCTCAGGAAAGGTGGTTTTATGTATCCAATTACCAGTGACTTCAGAAAATCAATCAAACTCACGAGGTACCAAAGTAAG
AATGTGGCAATCAGTTATGCAGAGTGTACAACTTCTCGACAACACTGTTTCCAGAATGGTGCACTTTAAGCTCTGCCCCT
CTACTATCATTAC

Alignment

ORF - retro_mmus_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.28 %
• Parental protein coverage: 88.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSTTVPGSSSGPLQNHQHVDNSSGRENVSDLTLGPGNSPITRMNTASGALSPLPRPNGTANSTKNLVV-T
          QSTTVPGSSSGPLQNHQHVD.SS..ENVS.LTL.PGNSP...MN......S..P.P......T....V..
Retrocopy QSTTVPGSSSGPLQNHQHVDSSSCMENVSNLTLVPGNSP---MNPPLQP*SLSPDPMELTANTSKNLVVS

Parental  AEMCCYCFDVLYCHLYGFPQPRLPRFTNDPYPLFVTWKTGRDKRLRGCIGTFSAMNLHSGLREYTLTSAL
          AEMCCYCFDVLYCHLYGFPQPRLPRF..DPYPLFVTWKTGRDK.L.GCIGTFSAMNLHSGL.EY.L.S.L
Retrocopy AEMCCYCFDVLYCHLYGFPQPRLPRFSSDPYPLFVTWKTGRDKWLCGCIGTFSAMNLHSGLSEYSLISVL

Parental  KDSRFPPLTREELPKLFCSVSLLTNFEDASDYLDWEVGVHGIRIEFINEKGIKRTATYLPEVAKEQDWDQ
          KDS.F.PLT.EELPKL.CSVSLLTNFEDASDY..WE.GVHG..IEFI.EKGIK.T.TYLPEVAKE.DWDQ
Retrocopy KDSQFLPLT*EELPKLVCSVSLLTNFEDASDYMNWEIGVHGKQIEFIKEKGIKHTTTYLPEVAKEYDWDQ

Parental  IQTIDSLLRKGGFKAPITSEFRKSIKLTRYRSEKVTISYAEYIASRQHCFQNGTLHAPPLYNHY
          IQT.DSLLRKGGF..PITS.FRKSIKLTRY.S..V.ISYAE...SRQHCFQNG.L.A.PLY.HY
Retrocopy IQTLDSLLRKGGFMYPITSDFRKSIKLTRYQSKNVAISYAECTTSRQHCFQNGAL*ALPLYYHY

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	26.38 RPM
SRP007412_cerebellum	0.00 RPM	33.65 RPM
SRP007412_heart	0.00 RPM	18.86 RPM
SRP007412_kidney	0.00 RPM	56.56 RPM
SRP007412_liver	0.00 RPM	59.12 RPM
SRP007412_testis	0.05 RPM	107.53 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_352 was not detected

EST

No EST(s) were mapped for retro_mmus_352 retrocopy.

TSS

No TSS is located nearby retro_mmus_352 retrocopy 5' end.

Lab

retro_mmus_352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_352 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009373	1 retrocopy	retro_chof_1566,
Callithrix jacchus	ENSCJAG00000010743	1 retrocopy	retro_cjac_383,
Equus caballus	ENSECAG00000023095	1 retrocopy	retro_ecab_1085,
Echinops telfairi	ENSETEG00000000510	1 retrocopy	retro_etel_9,
Homo sapiens	ENSG00000144233	1 retrocopy	retro_hsap_1227,
Gorilla gorilla	ENSGGOG00000014448	1 retrocopy	retro_ggor_961,
Myotis lucifugus	ENSMLUG00000006871	1 retrocopy	retro_mluc_684,
Macaca mulatta	ENSMMUG00000001987	1 retrocopy	retro_mmul_1302,
Mus musculus	ENSMUSG00000041915	2 retrocopies	retro_mmus_1330, retro_mmus_352 ,
Nomascus leucogenys	ENSNLEG00000015793	1 retrocopy	retro_nleu_700,
Pan troglodytes	ENSPTRG00000012437	1 retrocopy	retro_ptro_843,
Sarcophilus harrisii	ENSSHAG00000014762	1 retrocopy	retro_shar_86,