RetrogeneDB ID:

retro_ecab_20

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:7:59300000..59300522(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000005619
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PTP4A1
Ensembl ID:ENSECAG00000022483
Aliases:None
Description:protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]


Retrocopy-Parental alignment summary:






>retro_ecab_20
ATGGCTCCAATGAACTGCCTAGCCCCTGTGGAAGTCGCATACAGGAACATGAGATTTCTTATTACACACAATCCAACCAG
TGCAACCTTAAACAGATTTATAGAGGAACTTAAGGAATATGGAGTTACCACAATAGTAAGAGTATGTGAAGCAACTTATG
ACACTGCTGTCGTGGAGAAAGAAGGCATCCAGGTTCTGGATTGGCCTTTTGATGACGGCTCATCGCCCTCTAACCAGATT
GTTGATGACTGGTTAAGTCTTGTAAATAGTAAATTTCGTGAAGAACCTGGTTGTTGCATTGCCGTTCACTGTGTTACAGG
TCTTGGGAGAACTCCAGTGCTTGTTGCCCTAGCATTAATTGAAGGTGGGATGAAAAATGAAGATGCAGTACAGTTTATAA
GACAAAAGCGGCGGGGAGCTTTTAACAGCAAGCAACTTTTGTATTTGGAGAAATACCGTTCTAAAATGCGGCTGCGCTTC
AAAGACTCCTGGGGTCATAGAAACAACTGTTGCGTTCAATAA

ORF - retro_ecab_20 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.44 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPF
MA.MN..APVEV.Y.NMRFLITHNPT.ATLN.FIEELK.YGVTTIVRVCEATYDT..VEKEGI.VLDWPF
RetrocopyMAPMNCLAPVEVAYRNMRFLITHNPTSATLNRFIEELKEYGVTTIVRVCEATYDTAVVEKEGIQVLDWPF
ParentalDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGA
DDG..PSNQIVDDWLSLV..KFREEPGCCIAVHCV.GLGR.PVLVALALIEGGMK.EDAVQFIRQKRRGA
RetrocopyDDGSSPSNQIVDDWLSLVNSKFREEPGCCIAVHCVTGLGRTPVLVALALIEGGMKNEDAVQFIRQKRRGA
ParentalFNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCVQ
FNSKQLLYLEKYR.KMRLRFKDS.GHRNNCCVQ
RetrocopyFNSKQLLYLEKYRSKMRLRFKDSWGHRNNCCVQ

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
SRP021940_articular_cartilage 0 .00 RPM 17 .35 RPM
SRP021940_cerebellum 0 .00 RPM 22 .59 RPM
SRP021940_embryo 0 .03 RPM 45 .54 RPM
SRP021940_placental_villous 0 .05 RPM 52 .97 RPM
SRP021940_synovial_membrane 0 .03 RPM 14 .47 RPM
SRP021940_testis 27 .37 RPM 92 .27 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_20 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_20 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_20 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_807
Pan troglodytes retro_ptro_562
Gorilla gorilla retro_ggor_662
Pongo abelii retro_pabe_721
Callithrix jacchus retro_cjac_910
Mus musculus retro_mmus_3053
Rattus norvegicus retro_rnor_612
Oryctolagus cuniculus retro_ocun_225
Bos taurus retro_btau_1186
Canis familiaris retro_cfam_206
Parental genes homology:
Parental genes homology involve 18 parental genes, and 89 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000022753 retrocopies
retro_btau_1051, retro_btau_1186, retro_btau_859,
Equus caballus ENSECAG00000022483 6 retrocopies
retro_ecab_10, retro_ecab_1075, retro_ecab_20 , retro_ecab_425, retro_ecab_783, retro_ecab_869,
Echinops telfairi ENSETEG000000081836 retrocopies
retro_etel_1485, retro_etel_1681, retro_etel_1698, retro_etel_18, retro_etel_2153, retro_etel_668,
Latimeria chalumnae ENSLACG000000071831 retrocopy
retro_lcha_90,
Loxodonta africana ENSLAFG000000065728 retrocopies
retro_lafr_1054, retro_lafr_1120, retro_lafr_1133, retro_lafr_328, retro_lafr_670, retro_lafr_7, retro_lafr_780, retro_lafr_939,
Myotis lucifugus ENSMLUG000000011621 retrocopy
retro_mluc_264,
Macaca mulatta ENSMMUG000000027771 retrocopy
retro_mmul_1720,
Monodelphis domestica ENSMODG000000187015 retrocopies
retro_mdom_1630, retro_mdom_1864, retro_mdom_363, retro_mdom_729, retro_mdom_927,
Nomascus leucogenys ENSNLEG000000004406 retrocopies
retro_nleu_1111, retro_nleu_1159, retro_nleu_1681, retro_nleu_169, retro_nleu_407, retro_nleu_893,
Oryctolagus cuniculus ENSOCUG000000063114 retrocopies
retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
Ochotona princeps ENSOPRG000000049384 retrocopies
retro_opri_246, retro_opri_511, retro_opri_692, retro_opri_973,
Pongo abelii ENSPPYG000000167435 retrocopies
retro_pabe_2058, retro_pabe_255, retro_pabe_2660, retro_pabe_3732, retro_pabe_721,
Pteropus vampyrus ENSPVAG000000152252 retrocopies
retro_pvam_487, retro_pvam_848,
Rattus norvegicus ENSRNOG000000117714 retrocopies
retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus ENSRNOG000000463704 retrocopies
retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
Tupaia belangeri ENSTBEG0000000995614 retrocopies
retro_tbel_1216, retro_tbel_1392, retro_tbel_2167, retro_tbel_2236, retro_tbel_23, retro_tbel_2549, retro_tbel_2570, retro_tbel_2611, retro_tbel_3144, retro_tbel_3295, retro_tbel_3424, retro_tbel_4074, retro_tbel_4123, retro_tbel_869,
Tursiops truncatus ENSTTRG000000041296 retrocopies
retro_ttru_34, retro_ttru_450, retro_ttru_571, retro_ttru_642, retro_ttru_643, retro_ttru_69,
Vicugna pacos ENSVPAG000000042779 retrocopies
retro_vpac_167, retro_vpac_201, retro_vpac_275, retro_vpac_427, retro_vpac_476, retro_vpac_496, retro_vpac_535, retro_vpac_560, retro_vpac_583,


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