RetrogeneDB ID:

retro_mdom_888

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:319109639..319110622(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SEPT2
Ensembl ID:ENSMODG00000016041
Aliases:None
Description:septin 2 [Source:HGNC Symbol;Acc:7729]


Retrocopy-Parental alignment summary:






>retro_mdom_888
ATCAAGTCCAAATTTGAGTTCACTCTGATGGTGGTTGGGGAACCCGGCTTGGTTAAGTCTATGCTGATAAATAGCCTCTT
CTTGACTGGTCTGTACGCTGAAAGGGTCATTCCGGGGGCCGCAGAGAAAATAGAAAGGACTGTGCAGATTGAGGCCTCCA
CAGTGGAGATCAAGGAGAGAGGGGTCAAGCTCAGTCTCACTGTCGTAGACACACCGGCTATGGGGATGTGATTAACTGCG
GAGACTGTTTTAAGACCATCATCTCCTACATCGACAAGAAATTAGAAAGGTATCTGCAGGATGAAAGCAGTTTGAACCAG
CAACACATCATAGATAATCGGGTGCACTGCTGCTTCTACTTCATTTCACCTTTTGGATACGAGCTCAAACCATTAGATGT
TGAGTTTATGAAAGCAATCCACAATAAAGTGAATATCGTGCCCGTGATTGCAAAAGCTGATACTCTTACCCTGAAGAAGG
AACGATTGAAGAAGAGGGTCCTGGATGAAATCGAAGAGCGTGGCATCAAGATTTATCATTTGCCCGATGCTGAGTCCGAC
AAGGGCAAGGATTTCAAAGAACAGACTGGACTTCTGAAGGCCAGTATTCCGTTTTCAGTGATGGGATCCAATCAGCTGAT
TGAAGCCAAAGGCAAAAAGGTTCGAGGCCATCTTTATCCTTAGGGAGTCGTGGAAGTGGAGAATCCAGAACATAATGACT
TTCTCAAGCTGAGAACGATGCTAATCACTCACATGCAGGATTTCCAGGAGGTGACCCAGGATCTTTACCACGAGAACTTC
AGCTCGGAAAGAATCAAGAGAAGCGGCAGAAAAGTGGAAAATGAGGAAGTGAATCAAGACCAAATCTTGTTGGAAAAGGA
AGCAGAACTTTGTATGCAGGAGACTATCCAGAGGATGCAGGCTCAGATGCAGATGCAGATTCAAGGAGGAGGCAAGGATA
TCTTCGTGCATGGGCACCAGGCT

ORF - retro_mdom_888 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.24 %
Parental protein coverage: 91.44 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalVKKGFEFTLMVVGESGLGKSTLINSLFLTDLYPERVIPGAAEKIERTVQIEASTVEIEERGVKLRLTVVD
.K..FEFTLMVVGE.GL.KS.LINSLFLT.LY.ERVIPGAAEKIERTVQIEASTVEI.ERGVKL.LTVVD
RetrocopyIKSKFEFTLMVVGEPGLVKSMLINSLFLTGLYAERVIPGAAEKIERTVQIEASTVEIKERGVKLSLTVVD
ParentalTP-GYGDAINCRDCFKTIISYIDEQFERYLHDESGLNRRHIIDNRVHCCFYFISPFGHGLKPLDVEFMKA
TP.GYGD.INC.DCFKTIISYID...ERYL.DES.LN..HIIDNRVHCCFYFISPFG..LKPLDVEFMKA
RetrocopyTP<GYGDVINCGDCFKTIISYIDKKLERYLQDESSLNQQHIIDNRVHCCFYFISPFGYELKPLDVEFMKA
ParentalIHNKVNIVPVIAKADTLTLKERERLKKRVLDEIEEHGIKIYHLPDAESDEDEDFKEQTRLLKASIPFSVV
IHNKVNIVPVIAKADTLTLK..ERLKKRVLDEIEE.GIKIYHLPDAESD...DFKEQT.LLKASIPFSV.
RetrocopyIHNKVNIVPVIAKADTLTLK-KERLKKRVLDEIEERGIKIYHLPDAESDKGKDFKEQTGLLKASIPFSVM
ParentalGSNQLIEAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTMLITHMQDLQEVTQDLHYENFRSERLKRGGRL
GSNQLIEAKGKKVRG.LYP.GVVEVENPEHNDFLKLRTMLITHMQD.QEVTQDL..ENF.SER.KR.GR.
RetrocopyGSNQLIEAKGKKVRGHLYP*GVVEVENPEHNDFLKLRTMLITHMQDFQEVTQDLYHENFSSERIKRSGR-
ParentalKVENEEVNRDQILLEKEAELRRMQEMIARMQAQMQMQMQGGDGDIVMHGHQA
KVENEEVN.DQILLEKEAEL..MQE.I.RMQAQMQMQ.QGG..DI..HGHQA
RetrocopyKVENEEVNQDQILLEKEAEL-CMQETIQRMQAQMQMQIQGGGKDIFVHGHQA

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






RNA-Seq - click to see more details

(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 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_888 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_888 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 19 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000026081 retrocopy
retro_btau_1185,
Canis familiaris ENSCAFG000000129601 retrocopy
retro_cfam_1477,
Choloepus hoffmanni ENSCHOG000000087155 retrocopies
retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Callithrix jacchus ENSCJAG000000061221 retrocopy
retro_cjac_1501,
Cavia porcellus ENSCPOG000000136871 retrocopy
retro_cpor_845,
Loxodonta africana ENSLAFG000000119641 retrocopy
retro_lafr_4,
Macropus eugenii ENSMEUG000000165191 retrocopy
retro_meug_39,
Myotis lucifugus ENSMLUG000000071081 retrocopy
retro_mluc_1594,
Monodelphis domestica ENSMODG000000031041 retrocopy
retro_mdom_93,
Monodelphis domestica ENSMODG000000118251 retrocopy
retro_mdom_224,
Monodelphis domestica ENSMODG00000016041 1 retrocopy
retro_mdom_888 ,
Monodelphis domestica ENSMODG000000211671 retrocopy
retro_mdom_1672,
Mustela putorius furoENSMPUG000000001661 retrocopy
retro_mputfur_436,
Nomascus leucogenys ENSNLEG000000138731 retrocopy
retro_nleu_1848,
Otolemur garnettii ENSOGAG000000044571 retrocopy
retro_ogar_2239,
Pteropus vampyrus ENSPVAG000000005581 retrocopy
retro_pvam_448,
Rattus norvegicus ENSRNOG000000179521 retrocopy
retro_rnor_1110,
Ictidomys tridecemlineatus ENSSTOG000000133571 retrocopy
retro_itri_1227,
Drosophila melanogaster FBgn00117101 retrocopy
retro_dmel_35,


Copyright © RetrogeneDB 2014-2017