RetrogeneDB ID: retro_drer_9

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 4:11096568..11097441(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDARG00000032242
• Aliases: tnnt1, cb328, sb:cb328, stnt, zgc:86847
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: tnnt2a
• Ensembl ID: ENSDARG00000020610
• Aliases: tnnt2a, cTnT, tnnt2
• Description: troponin T2a, cardiac [Source:ZFIN;Acc:ZDB-GENE-000626-1]

Sequence

>retro_drer_9
ATGTGCGACACCGAAGAGTTTGTGGCAGAGTTCGAGGAGGAGGTGAAGGAGCAGGAAGCTGAGGAAGAGGAGGAAGCTGA
GGAAGAGGTTAAAGAAGAGGCTGAGGAGAAAGAAGAAGTTGAGGAAGAACAAGAAGAAGCTGAGGAAGGAGACGAACCTG
AAGAGACACATCAAGAAGAAGCAGACGATGAGCATGAAGCTGAAGAAGACACCAAACCCAAACCCAAGATGTTTGTTCCC
AACATTATACCACCAAAGCTGCCTGACGGGGAGAAGGTGGACTTTGATGACCTCCACCGGAAGCGTGTGGAGAAGGATTT
TAATGAACTGCAAAGCCTGATTAACCTGCACTTCACCACCAGGCAGAAGGAGGAGGATGAGCTGGTAGCGTTGAAGAACC
GAATTGAACGTCGTCGGACCGACCGTGCTGATCAGCAACGGATCAGAACTGAGCGAGACCGTGAAAGACAAGCACGCCTC
GCTGAAGAACGAGCCCGTCGTGAAGAGGAGGCCGCCAAATTGCGTGCCGAGGAAGATGCCAGGAAAAAGAAGATCCTTTC
CAACAAGGGCTACGGCGGCTTCCTGCAGAAGGTGGATCAGAAGAAAGGAAAGAAGCTGACCGAACGTGAGAAGAAGACCA
AATGTCTGCTAGAGCGTCGCAAGCCACTGAACATCGATCATCTCAACCAGGAGAAGCTGGGAGAGAAAGCTCTCGACCTG
TGGAAGTGGCTCAATCAGCTCCACGCTGAGAAGTTTGAGTTGGGAGAGAAGCTAAAGTCGCAGAAGTATGAGATCAAGGT
TTTGCGGAATCGAGTAAGTGACCATCAAAAGGGAACCAAGGTTGCGAAAACCACCAGGAAGTCCTGGAAGTAA

Alignment

ORF - retro_drer_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.04 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEVEEYEEQEEEQVEEEEEVQEEAQNDEEAQQEENAGGDEETTQEHDGEEETEDGGEEAKPKFLKPFMLP
          EEV.E.E..EEE..EEE.....E.....E..QEE...GDE................E..KPK.......P
Retrocopy EEVKEQEAEEEEEAEEEVKEEAEEKEEVEEEQEEAEEGDEPEETHQEEADDEHEAEEDTKPK--PKMFVP

Parental  NLVPPKIPDGERVDFDDIHRKRMEKDLNELQTLIEAHFESRKKEEEEIISLKDRIEKRRSERAEQQRIRS
          N..PPK.PDGE.VDFDD.HRKR.EKD.NELQ.LI..HF..R.KEE.E...LK.RIE.RR..RA.QQRIR.
Retrocopy NIIPPKLPDGEKVDFDDLHRKRVEKDFNELQSLINLHFTTRQKEEDELVALKNRIERRRTDRADQQRIRT

Parental  ERERERQKRLEEERARKEEEEAKKRAEDDAKKKKTLTSLHFGGYMQKIERRSGKKQTEREKKKKILGDRR
          ER.RERQ.RL.EERAR.EEE.AK.RAE.DA.KKK.L.....GG..QK.....GKK.TEREKK.K.L..RR
Retrocopy ERDRERQARLAEERARREEEAAKLRAEEDARKKKILSNKGYGGFLQKVDQKKGKKLTEREKKTKCLLERR

Parental  KPLDIDNANESALREKAKELWSWMRELEAEKFELQYQFGKQKYEINVLRNRVSDHQKRSKRTK
          KPL.ID..N...L.EKA..LW.W...L.AEKFEL......QKYEI.VLRNRVSDHQK..K..K
Retrocopy KPLNIDHLNQEKLGEKALDLWKWLNQLHAEKFELGEKLKSQKYEIKVLRNRVSDHQKGTKVAK

Legend:

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

Expression

RNA-Seq

Danio rerio was not studied using RNA-Seq expression data.

ChIP-Seq

Danio rerio was not studied using ChIP-Seq data.

EST

9 EST(s) were mapped to retro_drer_9 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI585194	11096773	11097108	98.3	329	6	323
CB363074	11096496	11096867	99.8	370	1	369
EB790284	11096496	11096960	99	460	2	457
EB832957	11096638	11096862	100	224	0	224
EB836672	11097017	11097137	100	120	0	120
EB855739	11096496	11096878	99.5	380	2	378
EB866493	11096499	11096873	100	374	0	374
EB962617	11096499	11096864	99.8	364	1	363
EB963725	11096496	11096881	99.8	383	1	382

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_9 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_9 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000020610	1 retrocopy	retro_drer_9 ,
Oreochromis niloticus	ENSONIG00000012310	1 retrocopy	retro_onil_9,
Oryzias latipes	ENSORLG00000006832	1 retrocopy	retro_olat_11,
Takifugu rubripes	ENSTRUG00000011858	1 retrocopy	retro_trub_31,