RetrogeneDB ID: retro_oana_3

Retrocopy location

• Organism: Platypus (Ornithorhynchus anatinus)
• Coordinates: Ultra516:4333799..4336787(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOANG00000003138
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TSHZ1
• Ensembl ID: ENSOANG00000001135
• Aliases: None
• Description: teashirt zinc finger homeobox 1 [Source:HGNC Symbol;Acc:10669]

Sequence

>retro_oana_3
TCAGTAGCTCAACTTCAGGGCGTCAATGACACTGGAACGGATGAGGAAGTAGAAACAGGCCCCGAGCAAAAAGGTAGCTT
TAGCTACCAGAACTCTCCAGGCAGTCATCTGTCTAATCAAGATGCAGAAAATGAATCTCTCTTGAGCGATGCCAGTGACC
AAGTGGCGGACATTAAAAGCAACTGCTGTAAAGATGCCCCGGAAAAGAAAACGAACGCCCACCCTAAACTTCAGAAGGAG
GCGCACAATTGCATGGATAAAATGACTGCAGTCTATGCCAACATCCTAACAGACTCCTATTGGACAGGCTTAGGGCTCGG
TCTCAAGTTATCTAACAGCGAACGGAGGAGCTGCGACAACCGCAATGGAGGCAATAAAAGTGACTTTGATTGGCACCAGG
ATGCTTTGTCAAAAAGCTTGCAACAGAGCCTACCTTCCAGACCCGTCTCCAAACCCAACCTTTTCAGTTCCGTCCAGTTG
TACAGGCAGAGCAGCAAAATGTGCGGAACGGTCTTCACGGGAGCCAGCCGGTTTCGGTGCAGACAGTGCAGTGCGGCGTA
CGACACCTTAGTCGAGTTAACAGTACACATGAATGAAACCGGTCACTACCAAGATGACAACCGCAAAAAAGACAAGCACA
GACCAACCAGCTACTCAAAGCCCCGAAAAAGGGCCTTTCAGGACATGGACAAAGAAGATGCACAAAAGGTCCTCAAATGT
ATGTTCTGTGGTGACTCCTTTGACTCCTTGCAAGATCTGAGTGTCCACATGATCAAAACAAAGCATTACCAAAAAGTGCC
TTTGAAGGAGCCCGTACCAACCATTTCTTCAAAAATGGTCACTCCTGCAAAGAAACGCGTTTTTGACGTCAACCGACCTT
GTTCCCCGGACTCTACCACCGGGTCTTTTGCCGATACGTTTTCTCCTCAGAAAAATGCCAACCTGCAGTTATCCTCTAAC
AACCGCTATGGCTACCAGAACGGGGCCAGCTATACCTGGCAGTTTGAGGCCTGCAAATCCCAGATCCTGAAGTGCATGGA
GTGCGGGAGTTCCCATGATACCTTGCAGCAGCTCACCACTCACATGATGGTCACAGGTCACTTTCTGAAGGTCACCAGTT
CTGCATCCAAGAAGGGGAAACAGCTGGTGCTCGATCCCCTGGCGGTAGAGAAAATGCAAACGTTGTCAGAGCCTCCAGCC
AGTGAGATCCCCGTGCCCAAGCCATCAAATAACACAGGATCAGACGGTGCAGTGTCTGCAGCGGAGCTAAAGAGTGAGAG
CAGAAAAGAAAAACCAGATGAAATCAACAAAGACGAGAAAGTGGTCAAAAATGAAGACTACGAGGACGCTCTTCAGAAAC
CGTTGGATCCTACAATGAAATACCAGTATCTTAGGGAGGAGGACTTAGAAGATGGATCCAAGGGAGGAGGGGACATTTTA
AAGTCATTAGAGAACACGGTGACCACAGCCATCAACAAAGCTCAGAACGGGGCTCCCAGTTGGAGCGCGTATCCTAGCAT
CCACGCAGCCTACCAGCTCTCCGAGGGGACAAAGCCCTCTCTGCCATTGGGCTCGCAGGTTCTGCAGATTAGACCAACGA
TCACCAATAAATTGAGGCCCATCGCTCCCAAGTGGAAGGTCATGCCTCTTGTCTCTGTCCCTGCAAATCTGGCCCAGGGC
ACCCAAGTTAAGAAGGAATCAGAAGACAGAGACGAAGGCCCGAGGGAATACACAAAGAGCAGTCCGCAACCTGAAGGTTC
CTCCCTCAGCCAGAGTGAGGGAGAGTCACTCCCCAAGAGCGAGAGCCCTTCAGACTCCAAAAAGACAGAGTCACCTCCCT
TGAAGGAGGAGGACAAAACAAAAGAAAACAGCGAGAAAGAAAAGCCAAAACTCAAGGATCCGACGTCTTCTCTCAGCAAC
GGCTGTGCCGCCGCCAGCCATCCCGGGGAACTGCCGGGCATCAACCCCCTCAGCGCCCTGCAGTCTGTGTTGAATAATCA
CCTGGGCAAGGCCACTGAGCCTCTGCGTTCTCAGGCCAGTTCAAGCCCCAGCTCTAGCACAATTTCTATGTTTCACAAGC
CAAACCTCAGCGTCATAGAGAAGCCGGTTCTGTCTCCTGCCCCATCGAGACCAGCGAGCGTGTCCAGGCATTACCTGTTT
GAAAGCAACGATCAGCCCATAGACCTGACCAAATCCAAAAGCAAGAAAACAGAGTCTGCCCAAGCGCAGTCGTGTACGTC
CCCGCCTCAGAAACACGCTCTGTCTGACATCGCCGACATGGTCAAAGTGCTTCCGAAAGCTACCACACCAAAACCTGCCA
CGTCTTCTAGGATCTCTTCCGTGAAGCTGGAAATGGACGTCAGGCGTTTTGAAGACGTCTCCACCGAAGTCTCCACGTTG
CATAAAAGAAAGGGCAGGCAGTCAAACTGGAATCCTCAGCACCTTCTGATTTTGCAAGCTCAGTTTGCCTCCAGCCTCTT
TCAGACGTCCGAAGGTAAATATTTGTTATCTGATTTAGGCCCGCAGGAGCGCATGCAGATTTCTAAGTTTACCGGACTGT
CTATGACCACCATTAGCCACTGGCTGGCAAATGTCAAGTATCAGCTTAGGAAAACTGGAGGGACTAAATTTTTGAAAAAC
ATGGACAAGGGGCACCCTATATTCTATTGCAGTGACTGTGCATCTCAGTTTAGAACCCCATCTACTTACATCAGCCACTT
AGAGTCCCACCTAGGTTTCCAAATGAAAGACATGAACAGGCTGGCAGTGGAACAGCAAACCAAGGTAGAGCAAGAAATCT
CCAGGGTATCTGTTCAAAGATCACCGGAAACAATAGCTGGGGAAGAGGACACAGACTCTAAATTCAAGTGTAAGTTGTGC
TGTCGGACATTTGCGAGCAAACACGCAGTAAAGCTTCATCTAAGCAAAACACACAGCAAGTCACCCGAACACCATTCACA
GTTTGTAGCAGAGGTGGATGAAGAATAG

Alignment

ORF - retro_oana_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.71 %
• Parental protein coverage: 52.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIKEAQSYQDSPVSTATNQEAGYGSPLSEGSDQQALFKTSSSKE--EKEESAGADGASYPQDSLAQIKAV
          E.K...SYQ.SP.S...NQ.A...S.LS..SDQ.A..K....K...EK...A................AV
Retrocopy EQKGSFSYQNSPGSHLSNQDAENESLLSDASDQVADIKSNCCKDAPEKKTNAHPKLQKEAHNCMDKMTAV

Parental  YANLLSDSCWSSLALDLKKSSPAASNSSTAGGGGGSGYDWHQAALAKTLQQTPSYGLLPEPSLFSTVQLY
          YAN.L.DS.W..L.L.LK.S...........GG..S..DWHQ.AL.K.LQQ.........P.LFS.VQLY
Retrocopy YANILTDSYWTGLGLGLKLSNSERRSCDNRNGGNKSDFDWHQDALSKSLQQSLPSRPVSKPNLFSSVQLY

Parental  RQNNKLYGSVFTGASKFRCKDCSAAYDTLVELTVHMNETGHYRDDNRDKEAEKTKRWSKPRKRSLMEMEG
          RQ..K..G.VFTGAS.FRC..CSAAYDTLVELTVHMNETGHY.DDNR.K........SKPRKR....M..
Retrocopy RQSSKMCGTVFTGASRFRCRQCSAAYDTLVELTVHMNETGHYQDDNRKKDKHRPTSYSKPRKRAFQDMD-

Parental  KEDAQKVLKCMYCGHSFESLQDLSVHMIKTKHYQKVPLKEPVPAITKLVPSTKKRALQDVASPGSPEATG
          KEDAQKVLKCM.CG.SF.SLQDLSVHMIKTKHYQKVPLKEPVP.I........K....DV..P.SP..T.
Retrocopy KEDAQKVLKCMFCGDSFDSLQDLSVHMIKTKHYQKVPLKEPVPTISSKMVTPAKKRVFDVNRPCSPDST-

Parental  PEAGPGPEAAKEPKAANPYVTPNNRYGYQNGASYTWQFEARKAQILKCMECGSSHDTLQQLTAHMMVTGH
          ...G.........K.AN.....NNRYGYQNGASYTWQFEA.K.QILKCMECGSSHDTLQQLT.HMMVTGH
Retrocopy --TGSFADTFSPQKNANLQLSSNNRYGYQNGASYTWQFEACKSQILKCMECGSSHDTLQQLTTHMMVTGH

Parental  FLKVTTSASKKGKQLVLDPTVEEKIQSIPLPPTTHTRLPASAPKKPPDSPAGDGAGDGVAEEKAKPEREQ
          FLKVT.SASKKGKQLVLDP...EK.Q....PP......P........D..................E...
Retrocopy FLKVTSSASKKGKQLVLDPLAVEKMQTLSEPPASEIPVPKPSNNTGSDGAVSAAELKSESRKEKPDEINK

Parental  EERVPATSQPERKIPERFEPATLYQYLREEDLGDSPRGGVDILKSLENTVSSAISKAQNGAPAWGGYPSI
          .E.V......E........P...YQYLREEDL.D...GG.DILKSLENTV..AI.KAQNGAP.W..YPSI
Retrocopy DEKVVKNEDYEDALQKPLDPTMKYQYLREEDLEDGSKGGGDILKSLENTVTTAINKAQNGAPSWSAYPSI

Parental  HAAYQLPGAAKP-LPPTAQSVQVQPSFAAGTKPLA
          HAAYQL....KP.LP...Q..Q..P.......P.A
Retrocopy HAAYQLSEGTKPSLPLGSQVLQIRPTITNKLRPIA

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	2.56 RPM	4.86 RPM
SRP007412_cerebellum	21.11 RPM	3.93 RPM
SRP007412_heart	1.86 RPM	7.53 RPM
SRP007412_kidney	11.25 RPM	2.07 RPM
SRP007412_liver	4.34 RPM	9.67 RPM
SRP007412_testis	58.47 RPM	5.93 RPM

ChIP-Seq

Ornithorhynchus anatinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_oana_3 retrocopy.

TSS

Ornithorhynchus anatinus was not studied using FANTOM5 data.

Lab

retro_oana_3 was not experimentally validated.

Homology

Retrocopy orthology:

Ornithorhynchus anatinus 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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003224	1 retrocopy	retro_cjac_17,
Ornithorhynchus anatinus	ENSOANG00000001135	1 retrocopy	retro_oana_3 ,