RetrogeneDB ID:

retro_mmus_2199

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:3:117176017..117176573(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Hmgb1
Ensembl ID:ENSMUSG00000066551
Aliases:Hmgb1, DEF, HMG-1, Hmg1, SBP-1, amphoterin, p30
Description:high mobility group box 1 [Source:MGI Symbol;Acc:MGI:96113]


Retrocopy-Parental alignment summary:






>retro_mmus_2199
ATAGGCAAAGGAGATCCTAAGAAGCCTAGAGGCAAAATGTTCTTATATGCATGCTTTGTGCAAACTGCTGGGAGAAGCAT
AAGAAAAAGCACCTGGATGCTTCTGTCAACTCTCAGAGTTCTCCAAGAAGTGCTCAGAGAGTAGAAGACCATGTTTGCTA
AAGAAAAGGGGAAACTGGAAGATATGACAAAGGCTGACAAGGCTCATTATGAAAGATAAATGAAAAACCTACATCCCCCC
TCCCAAGGGGAGACCAAAACGAAGTTCAAGGACTCCAGTACACCCAAGAGGTCTCATTCGGCCTTCTTCTTGTTCTGTTC
TGAATACCACTCCAAAATCAAAGGTGAGCATCATGGTTTATCCATTGGTGATGTTGCAAAGAAACTAGGAGAGATGTGAA
ACAATACTGCAGAGGATGGCAAACAGCCCTATGAGAAGAAGGCCACCAAACTGAAGGAGAAGTACGAGAAGGATATTGCT
GCCTACAGAGCTAAAGGAAAACCTGATGCAGCCAAAACGGGGGGTGGTCAAGGCTGAAAAGATCGAGAAAAAGAAG

ORF - retro_mmus_2199 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.95 %
Parental protein coverage: 86.05 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGKGDPKKPRGKMSSYAFFVQT-CREEHKKKHPDASVN-FSEFSKKCSERW-KTMSAKEKGKFEDMAKAD
.GKGDPKKPRGKM..YA.FVQT.C.E.HKKKH.DASVN..SEFSKKCSE...KTM.AKEKGK.EDM.KAD
RetrocopyIGKGDPKKPRGKMFLYACFVQT<CWEKHKKKHLDASVN<LSEFSKKCSESR<KTMFAKEKGKLEDMTKAD
ParentalKARYEREMKTYIPP-KGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNT
KA.YER.MK...PP..GETK.KFKD...PKR..SAFFLFCSEY..KIKGEH.GLSIGDVAKKLGEM.NNT
RetrocopyKAHYER*MKNLHPPSQGETKTKFKDSSTPKRSHSAFFLFCSEYHSKIKGEHHGLSIGDVAKKLGEM*NNT
ParentalAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAK-KGVVKAEKSKKKK
A.D.KQPYEKKA.KLKEKYEKDIAAYRAKGKPDAAK..GVVKAEK..KKK
RetrocopyAEDGKQPYEKKATKLKEKYEKDIAAYRAKGKPDAAK>RGVVKAEKIEKKK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 36 .52 RPM
SRP007412_cerebellum 0 .00 RPM 25 .49 RPM
SRP007412_heart 0 .00 RPM 35 .74 RPM
SRP007412_kidney 0 .00 RPM 43 .37 RPM
SRP007412_liver 0 .00 RPM 39 .30 RPM
SRP007412_testis 0 .00 RPM 12 .44 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2199 was not detected
No EST(s) were mapped for retro_mmus_2199 retrocopy.
No TSS is located nearby retro_mmus_2199 retrocopy 5' end.
retro_mmus_2199 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2199 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 17 parental genes, and 323 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000659713 retrocopies
Equus caballus ENSECAG000000084392 retrocopies
Felis catus ENSFCAG0000000020010 retrocopies
Homo sapiens ENSG0000018940337 retrocopies
Gorilla gorilla ENSGGOG0000002676423 retrocopies
Macropus eugenii ENSMEUG000000013802 retrocopies
Microcebus murinus ENSMICG000000071447 retrocopies
Macaca mulatta ENSMMUG000000233993 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Mus musculus ENSMUSG000000152171 retrocopy
Mus musculus ENSMUSG0000005471723 retrocopies
Mus musculus ENSMUSG00000066551 129 retrocopies
retro_mmus_1025, retro_mmus_1037, retro_mmus_1047, retro_mmus_1065, retro_mmus_1094, retro_mmus_1112, retro_mmus_1113, retro_mmus_1114, retro_mmus_1115, retro_mmus_1128, retro_mmus_1135, retro_mmus_1140, retro_mmus_1178, retro_mmus_1181, retro_mmus_1209, retro_mmus_1284, retro_mmus_1302, retro_mmus_1351, retro_mmus_1407, retro_mmus_1423, retro_mmus_1508, retro_mmus_1553, retro_mmus_1554, retro_mmus_1584, retro_mmus_1672, retro_mmus_1705, retro_mmus_1706, retro_mmus_1712, retro_mmus_1716, retro_mmus_1725, retro_mmus_1775, retro_mmus_1794, retro_mmus_1800, retro_mmus_1822, retro_mmus_1845, retro_mmus_1871, retro_mmus_1989, retro_mmus_2015, retro_mmus_2077, retro_mmus_2080, retro_mmus_2096, retro_mmus_2191, retro_mmus_2194, retro_mmus_2199 , retro_mmus_2209, retro_mmus_2224, retro_mmus_2229, retro_mmus_2280, retro_mmus_2300, retro_mmus_2324, retro_mmus_2404, retro_mmus_2407, retro_mmus_2409, retro_mmus_2414, retro_mmus_2420, retro_mmus_2425, retro_mmus_2467, retro_mmus_2469, retro_mmus_2524, retro_mmus_2532, retro_mmus_2627, retro_mmus_2670, retro_mmus_2682, retro_mmus_2702, retro_mmus_2719, retro_mmus_2754, retro_mmus_2789, retro_mmus_2815, retro_mmus_2823, retro_mmus_2866, retro_mmus_2877, retro_mmus_2886, retro_mmus_292, retro_mmus_2923, retro_mmus_2936, retro_mmus_2940, retro_mmus_2954, retro_mmus_2965, retro_mmus_2977, retro_mmus_303, retro_mmus_3046, retro_mmus_3056, retro_mmus_3059, retro_mmus_3067, retro_mmus_3070, retro_mmus_3075, retro_mmus_3102, retro_mmus_3106, retro_mmus_3121, retro_mmus_3169, retro_mmus_3175, retro_mmus_319, retro_mmus_3190, retro_mmus_3199, retro_mmus_3207, retro_mmus_3239, retro_mmus_3289, retro_mmus_3322, retro_mmus_3353, retro_mmus_3375, retro_mmus_3476, retro_mmus_3494, retro_mmus_3533, retro_mmus_359, retro_mmus_3612, retro_mmus_3676, retro_mmus_3692, retro_mmus_3715, retro_mmus_418, retro_mmus_515, retro_mmus_530, retro_mmus_574, retro_mmus_599, retro_mmus_618, retro_mmus_623, retro_mmus_624, retro_mmus_634, retro_mmus_704, retro_mmus_705, retro_mmus_785, retro_mmus_813, retro_mmus_839, retro_mmus_855, retro_mmus_881, retro_mmus_903, retro_mmus_906, retro_mmus_930, retro_mmus_965, retro_mmus_981,
Nomascus leucogenys ENSNLEG0000000072033 retrocopies
Rattus norvegicus ENSRNOG000000298131 retrocopy
Sorex araneus ENSSARG0000000447014 retrocopies
Sus scrofa ENSSSCG000000093273 retrocopies
Tursiops truncatus ENSTTRG000000103278 retrocopies



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