RetrogeneDB ID:

retro_cpor_711

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_249:661542..662253(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPH1
Ensembl ID:ENSCPOG00000001485
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_711
ATGATGCTGGGAGAAGATGATGAGGAGTTCGTGGTGAAGGTGCGGGGTTTGCCTTGGTCCTGCTCGGCTGACGAGGTGCA
GCGGTTCTTCTCCGACTGCAAAATTCAAAATGGTGCTCAAGGTATTTGTTTCATCTACACCAGAGAAGGCAGACCGAGTG
GCGAGGCTTTTGTTGAACTTGAATCCGAAGATGAAGTCAAACTAGCCCTGAAAAAAAGACAGAGAAACTATGGGACACAG
ATATGTTGAAGTATTCAAGTCAAACAACGTTGAAATGGATTGGGTGTTGAAGCATACTGGTCCAAATAGTCCTGACACGG
CCAATGATGGCTTTGTACGGCTTAGAGAACTCCCCTTTGGATGTAGCAAGGAAGAAATTGTTCAGTTCTTCTCAGGGTTG
GAAATCGTGCCAAATGGGATAACATTGCCAGTGGACTTCCAGGGGAGGAGTACAGGGGAGGCCTTCGTGCAGTTTGCTTC
ACAGGAAATAGCTGAAGAGGCTCTAAAGAAACACAAGGAGAGAATAGGGCACAGGTATATTGAGATCTTTACGAGCAGTC
GGCTGAAGTTAGAACTCACTATGACCCACCACAAAAGCTTATGGCCATGCAGCGGCCAGGCCCCTATGACAGACCTGGGG
CTGGCAGAGGGTATAACAGCATTGGCAGAGGAGCTAGCTTTGAGAGGATGAGGCGTGATGCCTACGGTGGA

ORF - retro_cpor_711 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.58 %
Parental protein coverage: 53.01 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMMLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
MMLG.E..E.FVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGI.FIYTREGRPSGEAFVELESEDEVKLA
RetrocopyMMLG-EDDEEFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGICFIYTREGRPSGEAFVELESEDEVKLA
ParentalLKK-DRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPN
LKK.DRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLR.LPFGCSKEEIVQFFSGLEIVPN
RetrocopyLKK>DRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRELPFGCSKEEIVQFFSGLEIVPN
ParentalGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR-AEVRTHYDPPRKLMAMQRPG
GITLPVDFQGRSTGEAFVQFASQEIAE.ALKKHKERIGHRYIEIF.SSR.AEVRTHYDPP.KLMAMQRPG
RetrocopyGITLPVDFQGRSTGEAFVQFASQEIAEEALKKHKERIGHRYIEIFTSSR<AEVRTHYDPPQKLMAMQRPG
ParentalPYDRPGAGRGYNSIGRGAGFERMRRGAYGG
PYDRPGAGRGYNSIGRGA.FERMRR.AYGG
RetrocopyPYDRPGAGRGYNSIGRGASFERMRRDAYGG

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
SRP017611_brain 0 .00 RPM 141 .49 RPM
SRP017611_kidney 0 .00 RPM 229 .06 RPM
SRP017611_liver 0 .00 RPM 90 .23 RPM
SRP040447_lung 0 .00 RPM 338 .31 RPM
SRP040447_skeletal_muscle 0 .00 RPM 85 .65 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_711 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_711 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus 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 22 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088882 retrocopies
retro_amel_57, retro_amel_9,
Bos taurus ENSBTAG000000093891 retrocopy
retro_btau_130,
Choloepus hoffmanni ENSCHOG000000038414 retrocopies
retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus ENSCJAG000000099311 retrocopy
retro_cjac_127,
Cavia porcellus ENSCPOG00000001485 5 retrocopies
retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711 ,
Equus caballus ENSECAG000000144291 retrocopy
retro_ecab_94,
Echinops telfairi ENSETEG000000113031 retrocopy
retro_etel_50,
Felis catus ENSFCAG000000012042 retrocopies
retro_fcat_131, retro_fcat_27,
Homo sapiens ENSG000001690452 retrocopies
retro_hsap_3322, retro_hsap_4911,
Myotis lucifugus ENSMLUG000000166251 retrocopy
retro_mluc_124,
Macaca mulatta ENSMMUG000000108431 retrocopy
retro_mmul_2,
Monodelphis domestica ENSMODG000000094363 retrocopies
retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Otolemur garnettii ENSOGAG000000126312 retrocopies
retro_ogar_208, retro_ogar_498,
Ochotona princeps ENSOPRG000000035131 retrocopy
retro_opri_11,
Procavia capensis ENSPCAG000000067151 retrocopy
retro_pcap_4,
Pongo abelii ENSPPYG000000161211 retrocopy
retro_pabe_110,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Rattus norvegicus ENSRNOG000000033991 retrocopy
retro_rnor_340,
Sorex araneus ENSSARG000000030241 retrocopy
retro_sara_29,
Sarcophilus harrisii ENSSHAG000000182041 retrocopy
retro_shar_674,
Sus scrofa ENSSSCG000000140221 retrocopy
retro_sscr_70,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,


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