RetrogeneDB ID: retro_tgut_30

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: Un:44829511..44831119(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTGUG00000015990
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSTGUG00000012340
• Aliases: None
• Description: SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]

Sequence

>retro_tgut_30
CTCAGCAGCTTTTTGCCAGCTCCAACCCAACTGTCCCCAGATCATCTGGAACTAGAAGAAAGAGCAAGAGCTCAGAGATC
CAGGCAGAGTGCTCTGGCCTCCTCACAAAGGGAACCTCCCCCATATGGTGACCGGAAGGGATGGATACCACAGGTGCTAG
AGGATTTTGGAGATGGGGGTGCCTTCCCAGAAATTCACGTGGCCCAATATCCATTGGATATGGGCCAAAAGAAGAAAATT
TCCAATGCTTTGGCTCTTCAGGTGGATGCAGAAGGAAAAATAAAATATGATGCAATTGCTCGACGAGGACAGTCAAAGGA
CAAGGTTATTTACACAAAGTACACAGATCTTGTGCCAAAAGAAGTCATGAATGTGGGTGATCCTGGACTGCAAAGACCAG
ATGACAAGGCAATTAGAGAGGTAACAAAGAAGACAAGAGCAGCCTTGGAGAAATTAATCTCCCAAAAAGTTGCAGCAGCC
ATGCCAGTTCGAGCTGCTGACGAGCCAGCTCTGGCACAGTACATTCGGTACACACCATCTCAGCAAGGAGCTGCATTCAA
CTCTGGAGCAAGGCAGAGAGTTATTCGGGTAGTGGAAATGCAGAAGGACCCTATGGAGCCTCCAAGATTCAAAATCAACA
AGAAGATTCCACGAGGACCACCATCTCCTCCAGCACCTGTAATGCACTCTCCGAGTAGAAAGATGACTGTGAGAGAGCAG
CAAGAGTGGAAAATTCCTCCATGCATTTCAAACTGGAAGAACGCAAAGGGTTACACCGTTCCCTTGGAGAAGCGTCTGGC
TGCAGATGGCAGAGGATTGCAGGCTGTTCATATTAATGAAAACTTTGCCAAACTTGCTGAGGCGCTCTATATTGCTGACA
GAAAGGCTCGTGAGGCAGTAGAGATGCGTGCCCAGTTGGAGAGGAAAATGGCTCAGAAAGAAAAGGAGAAACACGAGGAA
AAGCTCCGAGAAATGGCTCAGAAAGCCAGGGAGAGAAGAGCAGGGATCAAAACACGTGTTGAAAAAGAGGATGGAGCAGC
TAGAGAAAGGGATGAAATCAGACGTGACCGGCGCAAAGAAAGGCAACATGACAGAAATCTTTCCCGGGCAGCTCCTGATA
AAAGGTCAAAGCTGCAAAGGAATGAGAACAGAGATATCAGTGAAGTTATTGCCCTGGGGGTACCCAACCACAGGCCATCC
AATGAAATCCAATATGACCAGAGGCTGTTCAACCAGAGCAAGGGTATGGACAGTGGCTTTGCTGGTGGAGACGATGAAAT
TTATAATGTTTATGACCAGCCATGGAGAAGTGGCAAGGATATGGCCCAGAACATCTACAGGCCAAGTAAAAATATGGATA
AGGACATGTATGGTGATGATCTAGAGGCTCAAATAACGATCAGCAGGTTTGCTCCTGACAAAGAGTTTTCTAACTCAGAT
CGTAACACCGGAGGAAGGGGCAGAGATGGACCAGTTCAATTTGAGGAGGATCCATTTGGTTTGGACAAGTTTCTGGAAGA
AGCCAAGCAACACGGTGGTTCTAAACAGCCATCAGGCAGCAGCGGCCCTAAGGAACATGAGCATCAGAGCAAAAAGAGGA
GGAAGGAC

Alignment

ORF - retro_tgut_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.86 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSSFLPAPTQLSQDQLELEERARAQRSRQAALVSSRREPPPYGYRKGWIPRALEDFGDGGAFPEIHVAQY
          .SSFLPAPTQLS.D.LELEERARAQRSRQ.AL.SS.REPPPYG.RKGWIP..LEDFGDGGAFPEIHVAQY
Retrocopy LSSFLPAPTQLSPDHLELEERARAQRSRQSALASSQREPPPYGDRKGWIPQVLEDFGDGGAFPEIHVAQY

Parental  PLDMGRKKKMSNALAVQVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNVDDPELQRPDEEAIRE
          PLDMG.KKK.SNALA.QVDAEGKIKYDAIAR.GQSKDKVIY.KYTDLVPKEVMNV.DP.LQRPD..AIRE
Retrocopy PLDMGQKKKISNALALQVDAEGKIKYDAIARRGQSKDKVIYTKYTDLVPKEVMNVGDPGLQRPDDKAIRE

Parental  ITEKTRAALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRF
          .T.KTRAALEK..SQKVAAAMPVRAAD..A.AQYIRYTPSQQG.AFNSGA.QRVIR.VEMQKDPMEPPRF
Retrocopy VTKKTRAALEKLISQKVAAAMPVRAADEPALAQYIRYTPSQQGAAFNSGARQRVIRVVEMQKDPMEPPRF

Parental  KINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINE
          KINKKIPRGPPSPPAPVMHSPSRKMTV.EQQEWKIPPCISNWKNAKGYT.PL.KRLAADGRGLQ.VHINE
Retrocopy KINKKIPRGPPSPPAPVMHSPSRKMTVREQQEWKIPPCISNWKNAKGYTVPLEKRLAADGRGLQAVHINE

Parental  NFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARER
          NFAKLAEALYIADRKAREAVEMRAQ.ERKMAQKEKEKHEEKLREMAQKARERRAGIKT.VEKEDG.ARER
Retrocopy NFAKLAEALYIADRKAREAVEMRAQLERKMAQKEKEKHEEKLREMAQKARERRAGIKTRVEKEDGAARER

Parental  DEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRPSNEIQYDQRLFNQSKGMDSGF
          DEIR.DRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPN.RPSNEIQYDQRLFNQSKGMDSGF
Retrocopy DEIRRDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNHRPSNEIQYDQRLFNQSKGMDSGF

Parental  AGGEDEIYNVYDQPWRSGKDMAQNIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSNSDRNTRGRGRDG
          AGG.DEIYNVYDQPWRSGKDMAQNIYRPSKN.DKDMYGDDLEA.I...RF.PDKEFSNSDRNT.GRGRDG
Retrocopy AGGDDEIYNVYDQPWRSGKDMAQNIYRPSKNMDKDMYGDDLEAQITISRFAPDKEFSNSDRNTGGRGRDG

Parental  PVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHESKKRRKD
          PVQFEEDPFGLDKFLEEAKQHGGSK.PS.SS.PKEHEH.SKKRRKD
Retrocopy PVQFEEDPFGLDKFLEEAKQHGGSKQPSGSSGPKEHEHQSKKRRKD

Legend:

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

Expression

RNA-Seq

Taeniopygia guttata was not studied using RNA-Seq expression data.

ChIP-Seq

Taeniopygia guttata was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tgut_30 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_30 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_30 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Homo sapiens	ENSG00000100603	1 retrocopy	retro_hsap_174,
Gorilla gorilla	ENSGGOG00000026016	1 retrocopy	retro_ggor_257,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys	ENSNLEG00000016771	1 retrocopy	retro_nleu_982,
Otolemur garnettii	ENSOGAG00000029825	1 retrocopy	retro_ogar_1404,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Pan troglodytes	ENSPTRG00000006587	1 retrocopy	retro_ptro_165,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri	ENSTBEG00000014074	3 retrocopies	retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30 ,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,