RetrogeneDB ID: retro_tgut_18

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 2:58740472..58740902(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL27A
• Ensembl ID: ENSTGUG00000008355
• Aliases: None
• Description: ribosomal protein L27a [Source:HGNC Symbol;Acc:10329]

Sequence

>retro_tgut_18
CCTTTCAGACTGAGGGTCACCCAGAAGCTGAGAGGGCACATTAGCCACAGCCACATGCATATACAGGAAACATCCCAGAG
GACGTGGTAATGCTGGTGGTATGCAACATCACAGGATGAACTTTTACAAGTATCACTCCGGTTACTTCAGAAAAGTAGGC
ATGACACACTGTCACTTGAAAAGAAACCAAAAGTTCTGTGCTACTGTCAACTTGAAACTGTGGACAACTATAAGTGAATA
GAAAATGTTCAATTACATGAAAAATGAGGCCAGCCTGGCCTCAGTCACTGATACTATGCACTCAGGCTACTACAAAATAC
TGGGCAAGGGGAACCTGCACAAGCAACTCCCAGTTGTGAAAGCAAAGTTCTTCAGTTGAAGTCTATAGGGGAAAAAAATC
AAAGAAGTTGGTAGTGCCTGTGTGTTTGTG

Alignment

ORF - retro_tgut_18 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.51 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSRLRKTRKLRGHVSHGHGRV-GKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGMRHYHLKRNQKFC
          P.RLR.T.KLRGH.SH.H.....KH....G...NAGG..HHR.NF.KYH.GYF.KVGM.H.HLKRNQKFC
Retrocopy PFRLRVTQKLRGHISHSHMHI>RKHPRGRG---NAGGMQHHRMNFYKYHSGYFRKVGMTHCHLKRNQKFC

Parental  PTVNLDKLWTLVSEQTRLNYAKNEAGLAPVIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEK-IKE
          .TVNL.KLWT..SE....NY.KNEA.LA.V.D...SGYYK.LGKG.L.KQ...VKAKFFS.....K.IKE
Retrocopy ATVNL-KLWTTISE*KMFNYMKNEASLASVTDTMHSGYYKILGKGNLHKQLPVVKAKFFS*SL*GKKIKE

Parental  VGGACVLV
          VG.ACV.V
Retrocopy VGSACVFV

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_18 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_18 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 90 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004205	15 retrocopies	retro_amel_1095, retro_amel_1160, retro_amel_1165, retro_amel_130, retro_amel_1311, retro_amel_1441, retro_amel_1673, retro_amel_393, retro_amel_450, retro_amel_497, retro_amel_521, retro_amel_693, retro_amel_752, retro_amel_966, retro_amel_989,
Bos taurus	ENSBTAG00000005349	2 retrocopies	retro_btau_126, retro_btau_45,
Canis familiaris	ENSCAFG00000006936	2 retrocopies	retro_cfam_145, retro_cfam_384,
Callithrix jacchus	ENSCJAG00000011775	1 retrocopy	retro_cjac_211,
Ficedula albicollis	ENSFALG00000000924	1 retrocopy	retro_falb_20,
Felis catus	ENSFCAG00000008411	13 retrocopies	retro_fcat_1162, retro_fcat_1285, retro_fcat_1305, retro_fcat_1380, retro_fcat_1635, retro_fcat_1761, retro_fcat_1805, retro_fcat_1974, retro_fcat_469, retro_fcat_652, retro_fcat_673, retro_fcat_817, retro_fcat_907,
Gorilla gorilla	ENSGGOG00000001660	2 retrocopies	retro_ggor_155, retro_ggor_1785,
Loxodonta africana	ENSLAFG00000000425	2 retrocopies	retro_lafr_25, retro_lafr_50,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Macaca mulatta	ENSMMUG00000021828	2 retrocopies	retro_mmul_207, retro_mmul_268,
Mustela putorius furo	ENSMPUG00000012532	3 retrocopies	retro_mputfur_118, retro_mputfur_1362, retro_mputfur_464,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Nomascus leucogenys	ENSNLEG00000017535	1 retrocopy	retro_nleu_102,
Oryctolagus cuniculus	ENSOCUG00000005442	1 retrocopy	retro_ocun_12,
Pan troglodytes	ENSPTRG00000003333	1 retrocopy	retro_ptro_33,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Sus scrofa	ENSSSCG00000014569	9 retrocopies	retro_sscr_527, retro_sscr_574, retro_sscr_587, retro_sscr_588, retro_sscr_644, retro_sscr_668, retro_sscr_677, retro_sscr_769, retro_sscr_809,
Taeniopygia guttata	ENSTGUG00000008355	1 retrocopy	retro_tgut_18 ,
Tarsius syrichta	ENSTSYG00000013207	16 retrocopies	retro_tsyr_1103, retro_tsyr_155, retro_tsyr_1591, retro_tsyr_1607, retro_tsyr_1623, retro_tsyr_170, retro_tsyr_1725, retro_tsyr_187, retro_tsyr_204, retro_tsyr_283, retro_tsyr_498, retro_tsyr_50, retro_tsyr_550, retro_tsyr_608, retro_tsyr_612, retro_tsyr_716,