>retro_cjac_2016
AATGCCGTTTCTAAGTACCAGGAAGTCACAAATAATTTGGAGTTTGCAAAAGAATTACAGAGGAGTTTCATGGCACTAAG
TCAAGATATTCAGAAAACAATAAAGAAGACAGCACCTCGGGAGCAGCTTATGAGAGAAGAAGCTGAACAGAAACGTTTAA
AAACTGTACTTGAGTTACAGTATGTTTTGGACGAATTGGGAAACGACGAAGTGCGAACTGACCTGAAACAAGGTTCGAAT
GGAGTGCCTATATTGTCCGAAGAGGAATTGTCATTGTTGGATGAATTCTGTAGGTTAGTAGACCCTGAACGGGACGTGAG
CTTGAGGTTGAATGAACAGTGTGAACATGCCTCCATTCACCTGTGGGTCCTGCTGGAAGGGAAGGAAAAATCTGTATGTG
GAATCACCTGTAAAGTTCTAAAAGACATTGTCGAGTGTGTTTTTCAATGAAACTACTTTGACAGCACCCACAACCACCAG
AATGGGTTGTGTGAGGAAGAAGAGGCAGCCTCAGCACCTACAATTGAAGACCAGGTAGCTGAAGCTGAACCTGAGCCAGT
GGAAGACTACACTGAGCAAAATGAAGTTGAGTCAGCAGAGTATGTAAATAGACAGTTCATGGCAGAAACACAGTTCACCA
GTGGCGAAAAGGAGCAGGTAGATGAGTGGGCAGTTGAAACAGTTGAGGTGGTAGATTCATTCCAGCAGCAGCCTCAGGCT
TCATCCCCTTCAGTACCACAACCCCACTCTTTGACTCCTGTGGCTCAAGCAGATCCCCTTCTGAGAAGACAGCGAGTACA
GGACCTTATGGCACAAATGCAGGGTCCCTATAATTTCGTACAGGATTCAGTGCTGGATTTTGAAAACCAGACACTTGATC
CTGCCATTGTATCTGCACAGCCTGTGAGTCCAGCACAAAACATGGGCATGCCCCAGCTGGTTTGCCCTCCACTTCATTCT
GAATCTAGACTTGCTCAGCCTATCAAGTTCCTGTACAACCAGAAGCTACACGGGTTCCTCTGGTGTCATCCACAAGTGAG
GGGTATACGGCATCTCAACGCCTGTACCAGCCTTCTCCTGCTACAGAGCCACGACCACAGAAGGAACCAATTGATCAGAT
TCAGGCAACAATCTCTTTAAATACAGACCGGATTACAGCATTATGATCCCTTCCTGATGCTTCTCAGCCCCAAGTACTTC
AGGCTGGGACAAGCAAACCTTTATGTAGTGGTGGAATCAATGTAAATGCAGCTCCATTCTAATCCATGCAAACGGTGTTC
AGTATGAATGCCCCAGTTCCTCCAGTTAATGAACCAGAAACTTTAATACAGCAAACTCAGTACCAGGCCAGTTATAACCA
GAGCTTTTCTAGTCAGTCTCACCAAGTAGAACAAACA
ORF - retro_cjac_2016 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
88.7 % |
Parental protein coverage: |
71.89 % |
Number of stop codons detected: |
3 |
Number of frameshifts detected |
1 |
Retrocopy - Parental Gene Alignment:
Parental | DAVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTARREQLMREEAEQKRLKTVLELQYVLDKLGDDE |
| .AVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTA.REQLMREEAEQKRLKTVLELQYVLD.LG.DE |
Retrocopy | NAVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTAPREQLMREEAEQKRLKTVLELQYVLDELGNDE |
|
Parental | VRTDLKQGLNGVPILSEEELSLLDEFYKLVDPERDMSLSKRLNEQYEHASIHLWDLLEGKEKSVCGTTYK |
| VRTDLKQG.NGVPILSEEELSLLDEF..LVDPERD.SL..RLNEQ.EHASIHLW.LLEGKEKSVCG.T.K |
Retrocopy | VRTDLKQGSNGVPILSEEELSLLDEFCRLVDPERDVSL--RLNEQCEHASIHLWVLLEGKEKSVCGITCK |
|
Parental | VLKEIVERVFQSNYFDSTHNHQNGLCEEEEAASAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVNRQFMA |
| VLK.IVE.VFQ.NYFDSTHNHQNGLCEEEEAASAPT.EDQVAEAEPEP.E.YTEQNEVES.EYVNRQFMA |
Retrocopy | VLKDIVECVFQ*NYFDSTHNHQNGLCEEEEAASAPTIEDQVAEAEPEPVEDYTEQNEVESAEYVNRQFMA |
|
Parental | ETQFTSGEKEQVDEWTVETVEVVNSLQQQPQAASPSVPEPHSLTPVAQADPLVRRQRVQDLMAQMQGPYN |
| ETQFTSGEKEQVDEW.VETVEVV.S.QQQPQA.SPSVP.PHSLTPVAQADPL.RRQRVQDLMAQMQGPYN |
Retrocopy | ETQFTSGEKEQVDEWAVETVEVVDSFQQQPQASSPSVPQPHSLTPVAQADPLLRRQRVQDLMAQMQGPYN |
|
Parental | FIQDSMLDFENQTLDPAIVSAQPMNPAQNMDMPQLVCPPVHSESRLAQP-NQVPVQPEATQVPLVSSTSE |
| F.QDS.LDFENQTLDPAIVSAQP..PAQNM.MPQLVCPP.HSESRLAQP..QVPVQPEAT.VPLVSSTSE |
Retrocopy | FVQDSVLDFENQTLDPAIVSAQPVSPAQNMGMPQLVCPPLHSESRLAQP<YQVPVQPEATRVPLVSSTSE |
|
Parental | GYTGSQPLYQPSHATEQRPQKEPIDQIQATISLNTDQTTASSSLPAASQPQVFQAGTSKPLHSSGINVNA |
| GYT.SQ.LYQPS.ATE.RPQKEPIDQIQATISLNTD..TA..SLP.ASQPQV.QAGTSKPL.S.GINVNA |
Retrocopy | GYTASQRLYQPSPATEPRPQKEPIDQIQATISLNTDRITAL*SLPDASQPQVLQAGTSKPLCSGGINVNA |
|
Parental | APFQSMQTVFNMNAPVPPVNEPETLKQQNQYQASYNQSFSSQPHQVEQT |
| APF.SMQTVF.MNAPVPPVNEPETL.QQ.QYQASYNQSFSSQ.HQVEQT |
Retrocopy | APF*SMQTVFSMNAPVPPVNEPETLIQQTQYQASYNQSFSSQSHQVEQT |
|
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 |
SRP051959_colon |
3 .37 RPM |
113 .20 RPM |
SRP051959_heart |
2 .21 RPM |
74 .34 RPM |
SRP051959_kidney |
3 .28 RPM |
114 .37 RPM |
SRP051959_liver |
2 .12 RPM |
78 .35 RPM |
SRP051959_lung |
3 .14 RPM |
110 .08 RPM |
SRP051959_lymph_node |
3 .38 RPM |
107 .26 RPM |
SRP051959_skeletal_muscle |
0 .59 RPM |
43 .68 RPM |
SRP051959_spleen |
2 .92 RPM |
120 .74 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2016 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2016 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2016 has 0 orthologous retrocopies within eutheria group .
Parental genes homology:
Parental genes homology involve
1 parental gene, and
4 retrocopies.