RetrogeneDB ID: retro_tgut_13

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 1:10321819..10322538(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38A
• Ensembl ID: ENSTGUG00000008995
• Aliases: None
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing A [Source:HGNC Symbol;Acc:25930]

Sequence

>retro_tgut_13
CTGGTGCTGGACAAGGCCATGGAGCTCGAGTGCATGGGGGTGTCTATGGAGGGAGCATTAAACCCATTAAACCCATCTTG
TGCCTGATGCTGAAGATGCTGCAGATCCAGCCCAAGAAGGGCATCACTGTGGAGTTCCTAAAGAATGAGGACGTCAAGGA
TGTCCAAATGCTTGGAGAGGTGTCCATGAGGCTGGCAGGCACTGCCATCGATGGCTACAGGTACCTGGAACCACTGAACA
GTGACTGCTGGAGAATAAAACACCAGGACAGGAAAGGGGGATGTGAGCAGATGCACAGGGATGAATTTAGTGATGAGCTG
CTCCATGAAGAACGTGTATGCAATGTCATCCTGCCTTGGCTGCAGAAATGACACGTTCTGGAAGGAGCTGAGCAACTCCA
GCCTCGAGTTAGTGCTCTGGAAGAAGACATGCCTGATGCAGAATCGAATCAGGAAAAGATGCAAAGCTGGAATGAATCCC
ATCTCCAGATCACTGCAGGAGGGGGCAGAGAGACCTGGACAAGCAGATCTGCAGTGGGGCAGTGCAGGTGGGGCTGGAGC
AGGTCTGCAGGGAGGCACAGCTGCTCTCCAAAGAGAAGAGCCCCTCACTGTGCCAGGAGAGGCATTGCAGCAAAAGCCTG
AGATGGCACCAGAGCAGATCCTGGAGAGGCAGCACAGATCAAGATTTAATCTCCAGCACATGACCACAGTCACAGACAC

Alignment

ORF - retro_tgut_13 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.3 %
• Parental protein coverage: 78.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LVVDKAMELKYVG-GVYGGNIKPTPF-LCLTLKMLQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTGTA
          LV.DKAMEL...G.GVYGG........LCL.LKMLQIQP.K.I.VEF.KNED.K.V.MLG...MRL.GTA
Retrocopy LVLDKAMELECMG<GVYGGXXXXXXXXLCLMLKMLQIQPKKGITVEFLKNEDVKDVQMLGEVSMRLAGTA

Parental  IDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHEERVCDIILPRLQKRYVLEEAEQLEPRVSA
          ID.Y.YLEPL..D...IK.Q.R.G..E.MH.DEF.DELLHEERVC..ILP.LQK..VLE.AEQL.PRVSA
Retrocopy IDGYRYLEPLNSDCWRIKHQDRKGGCEQMHRDEFSDELLHEERVCNVILPWLQK*HVLEGAEQLQPRVSA

Parental  LEEDMDDVESSEEEEEE-DEKLERIPSPDHRRRGYRDLDKPRRSPVV-RYRRSRSRSPRRRSRSPKRR-S
          LEE...D....E...E..D.KLE.IPSPDH.RRG.RDLDK...S..V.R...SRS....R.S.SPKRR.S
Retrocopy LEE---DMPDAESNQEK<DAKLE*IPSPDHCRRGQRDLDKQICSGAV>RWGWSRSAG--RHSCSPKRR<S

Parental  PSPRRERHRSKSPRRHRSRS-RERRHRSRSK-SPGHHRSHRH
          PS...ERH.SKS.R.H.SRS..ER.HRSR...SP.H..SHRH
Retrocopy PSLCQERHCSKSLRWHQSRS<LERQHRSRFN<SPAHDHSHRH

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_13 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_13 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13 , retro_tgut_14,