RetrogeneDB ID:

retro_btau_130

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:55239201..55240551(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000007499
Aliases:HNRNPH2, HNRPH2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:BT.49851
Ensembl ID:ENSBTAG00000009389
Aliases:HNRNPH1, HNRPH1
Description:heterogeneous nuclear ribonucleoprotein H [Source:RefSeq peptide;Acc:NP_001180163]


Retrocopy-Parental alignment summary:






>retro_btau_130
ATGATGCTGAGCACAGAAGGCAGGGAGGGGTTCGTGGTGAAGGTCAGGGGCCTGCCCTGGTCCTGCTCAGCTGATGAAGT
GATGCGCTTCTTCTCCGATTGTAAAATCCAAAATGGCACATCAGGTATTCGTTTCATCTACACCAGAGAAGGCAGACCAA
GTGGTGAAGCATTTGTCGAACTTGAGTCTGAAGATGAAGTGAAATTGGCTCTGAAGAAGGACAGAGAAACCATGGGACAC
AGATATGTTGAAGTATTCAAGTCCAACAGTGTTGAAATGGATTGGGTGTTGAAGCACACAGGTCCGAATAGTCCTGATAC
TGCCAATGATGGCTTCGTCCGGCTTAGAGGACTCCCATTTGGCTGTAGCAAGGAAGAGATTGTTCAGTTCTTTTCAGGGT
TGGAAATTGTGCCAAATGGGATGACACTGCCGGTGGACTTTCAGGGGCGGAGCACAGGGGAGGCCTTTGTGCAATTTGCT
TCGCAGGAGATAGCTGAAAAGGCCTTAAAGAAACACAAGGAAAGAATAGGGCACCGGTACATTGAAATCTTCAAGAGTAG
CCGAGCTGAAGTCCGAACCCATTATGACCCCCCTCGAAAGCTCATGGCTATGCAGCGGCCAGGTCCCTATGACAGGCCAG
GGGCTGGCAGAGGGTATAATAGCATTGGCAGAGGGGCTGGTTTTGAAAGGATGAGGAGGGGTGCCTATGGTGGAGGGTAT
GGAGGCTATGACGACTATGGTGGCTATAATGATGGATATGGCTTTGGATCTGATAGATTTGGAAGAGACCTGAATTACTG
TTTTTCAGGAATGTCTGATCATAGATATGGAGATGGTGGGTCCAGTTTTCAGAGCACCACAGGGCACTGTGTACACATGA
GGGGATTACCTTACAGAGCCACTGAGAATGATATTTACAATTTCTTCTCACCTCTTAATCCCATGAGAGTACACATTGAA
ATTGGACCTGATGGCAGAGTTACTGGTGAGGCAGATGTTGAATTTGCTACTCATGAAGATGCTGTGGCAGCTATGGCAAA
AGACAAAGCTAACATGCAACACAGATACGTGGAGCTCTTCTTGAATTCTACCGCAGGCACGAGTGGGGGAGCCTATGATC
ACAGCTACGTAGAACTCTTTTTGAATTCTACAGCCGGGGCAAGTGGTGGAGCTTATGGTAGCCAAATGATGGGAGGCATG
GGCATATCCAACCAGTCTAGTTACGGAGGTCCTGCCAGTCAGCAGCTGAGTGGTGGTTACGGAGGTGGATATGGTGGTCA
GAGTAGTATGAGTGGATATGACCAAGTTCTGCAGGAAAACTCCAGTGACTATCAATCAAACCTCGCTTAG

ORF - retro_btau_130 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.84 %
Parental protein coverage: 94.49 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMMLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
MML.TEG.EGFVVKVRGLPWSCSADEV.RFFSDCKIQNG..GIRFIYTREGRPSGEAFVELESEDEVKLA
RetrocopyMMLSTEGREGFVVKVRGLPWSCSADEVMRFFSDCKIQNGTSGIRFIYTREGRPSGEAFVELESEDEVKLA
ParentalLKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
LKKDRETMGHRYVEVFKSN.VEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
RetrocopyLKKDRETMGHRYVEVFKSNSVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
ParentalITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
.TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
RetrocopyMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
ParentalDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
DRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDY.GYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
RetrocopyDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYGGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
ParentalSTFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKA
S.FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP.RVHIEIGPDGRVTGEADVEFATHEDAVAAM.KDKA
RetrocopySSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKA
ParentalNMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGY
NMQHRYVELFLNSTAG.SGGAY.H.YVELFLNSTAGASGGAYGSQMMGGMG.SNQSSYGGPASQQLSGGY
RetrocopyNMQHRYVELFLNSTAGTSGGAYDHSYVELFLNSTAGASGGAYGSQMMGGMGISNQSSYGGPASQQLSGGY
ParentalGGGYGGQSSMSGYGSQGAVNSSYYSS
GGGYGGQSSMSGY......NSS.Y.S
RetrocopyGGGYGGQSSMSGYDQVLQENSSDYQS

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
ERP005899_liver 13 .63 RPM 365 .38 RPM
ERP005899_muscle 39 .59 RPM 169 .72 RPM
SRP017611_brain 37 .87 RPM 202 .63 RPM
SRP017611_kidney 48 .72 RPM 325 .58 RPM
SRP017611_liver 26 .96 RPM 108 .73 RPM
SRP030211_testis 9 .02 RPM 306 .76 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

5 EST(s) were mapped to retro_btau_130 retrocopy
EST ID Start End Identity Match Mis-match Score
DY071358 55239401 55239956 97.7 207 5 201
DY102973 55240104 55240337 100 233 0 233
DY139957 55239658 55239909 99.3 249 2 247
DY156677 55240104 55240311 99.1 205 2 203
GH314037 55239146 55239834 100 688 0 688

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_130 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_130 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Equus caballus retro_ecab_94
Parental genes homology:
Parental genes homology involve 32 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088882 retrocopies
retro_amel_57, retro_amel_9,
Bos taurus ENSBTAG00000009389 1 retrocopy
retro_btau_130 ,
Bos taurus ENSBTAG000000143162 retrocopies
retro_btau_1504, retro_btau_470,
Bos taurus ENSBTAG000000205131 retrocopy
retro_btau_42,
Bos taurus ENSBTAG000000218381 retrocopy
retro_btau_847,
Canis familiaris ENSCAFG000000003362 retrocopies
retro_cfam_200, retro_cfam_230,
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 ENSCPOG000000014855 retrocopies
retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711,
Dipodomys ordii ENSDORG000000054531 retrocopy
retro_dord_3,
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,
Gorilla gorilla ENSGGOG000000258442 retrocopies
retro_ggor_1299, retro_ggor_177,
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,
Mustela putorius furoENSMPUG000000006931 retrocopy
retro_mputfur_156,
Mus musculus ENSMUSG000000078501 retrocopy
retro_mmus_142,
Nomascus leucogenys ENSNLEG000000266583 retrocopies
retro_nleu_1668, retro_nleu_28, retro_nleu_48,
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,
Ictidomys tridecemlineatus ENSSTOG000000163762 retrocopies
retro_itri_66, retro_itri_78,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,


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