RetrogeneDB ID: retro_gacu_19

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXI:14371007..14372508(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000014124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: elfn1b
• Ensembl ID: ENSGACG00000016502
• Aliases: None
• Description: extracellular leucine-rich repeat and fibronectin type III domain containing 1b [Source:ZFIN;Acc:ZDB-GENE-080327-21]

Sequence

>retro_gacu_19
AGTGCCTTGTTTTGGTCCGTAGCCATTGTGTATTTGACTAACATCGGCAGAGTCAGCGGAGACTGCTGGTTAATTGAGGG
TGAAAAGGGCTTTGTGTGGCTTGCGATTTGTAGCCAAAACCAACCACCTTATGAGGCCATCCCACAGCATATCAACAGCA
CCATTGTGGACCTCCGTCTGAATGAAAACAAAATCAAAAGCATCCATTATTCTGCCCTCAGTCGCTTTGCCAACTTGACC
TACCTGAACCTGACGAAGAATGAAATCTCCTACATAGAGGATGGGGCCTTTTCTGCTCAGTTCAACTTACAAGTCCTCCA
AATGGGCTTCAACAAGTTGCGCAACCTGACGGAGGGGGTCCTCAGGGGTTTGGGAAAGCTGCAGTACCTCTACCTCCAGG
CAAACCTGATTGAGACCGTGACACCCAATGCCTTTTGGGAATGCCCCAACATAGAGAACATTGACCTCTCCATGAACCGA
ATCCAGCAGCTGGACGGGTCCACGTTTACCAGTCTGACCAAACTGACCACCTGCGAGCTGTACACCAACCCCTTCAACTG
CTCGTGCGAACTGCTGGGTTTTGTCAAATGGCTCTCGGTTTTCCCAAACCGGACGAACGAGCGGATGGTCTGCGACTCCC
CACCCGGCGTCTCCGGCTACAGCTTACTGAGCCCGAATCCCAACAATCCGACGTTTCGCAACGCGCTGCACATGCTCACC
ACCGTGTGCACGGACGACTACGTGACGCCGTTCATCCCCGTGCCCACCGAGTCCTCGACACCCCCGCCGGACCTGACGCT
GTGCGGGGCTGGAAGACTGTCCCTCGGGCACAGAGCCGGAAGACATCACCATCAGCACCTACAACGTGGTGGAGGTGAAC
CCTCTGATGAAGCTGAAGCAGGTATCGAACACAGGCGCCACCGTCACGGTTCAGATCCCTCACCCCTTCAAGAAGATGTA
CATCCTGTCTCTGTACAACAACAGCTTTTTCAGCGACATTCAAACCCTGAAAGCTTCGAAAGAGGACGTGGAACTGAAAA
ACCTCAAACCCCACACCAACTACACGTACTGTGTGTGTTCCATACGCAACTCGCTGAGACACAACCACACCTGCCTGACC
ATCACCACCGGCACTCTGAAGGGGAAGGCCAGAGACGTGAACAACGCGACCGCCACTCACTACATCATGACGATTTTGGG
CTGCCTCTTCAGCATGGTCATCTTCCTGGGCGTGGTCTACTACTGCTTGCGTCGAAAGCGCCAGCAAGACGAAAAGCACA
AAAGAGCCGGCAGCCTGAAGAAGAACATAATCGAGCTCAAATACGGACAAGAGCTCGAGGGCGCGACCGTTTCTCGAATG
TCGCAGAAGCAGCTGTTGGCCGGCGAGAGCATGGCACGAATGCCCTACTTGCCATCTGCGGCTGAAATGGAGCAGTACAA
ATTCCAGGAGATGAGTGACACTCCTAAGATGATGAAAGGGAATTACATGGACGTGCGCGGC

Alignment

ORF - retro_gacu_19 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.82 %
• Parental protein coverage: 60.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFLRW-LALLSMVRLPTATADCWLIEGEKGFVWLAICSMNQPPYEAIPSHINSTIVDLRLNENKIRSVHY
          S.L.W..A............DCWLIEGEKGFVWLAICS.NQPPYEAIP.HINSTIVDLRLNENKI.S.HY
Retrocopy SALFWSVAIVYLTNIGRVSGDCWLIEGEKGFVWLAICSQNQPPYEAIPQHINSTIVDLRLNENKIKSIHY

Parental  SSLSRFGNLTYLNLTKNDISYVEDGAFSAQFNLQVLQMGFNKLRNLTEGMLRGLGKLQYLYLQANLIETV
          S.LSRF.NLTYLNLTKN.ISY.EDGAFSAQFNLQVLQMGFNKLRNLTEG.LRGLGKLQYLYLQANLIETV
Retrocopy SALSRFANLTYLNLTKNEISYIEDGAFSAQFNLQVLQMGFNKLRNLTEGVLRGLGKLQYLYLQANLIETV

Parental  TPNTFWECPNIENIDLSMNRIQVLDGGLFSGLSKLTTCELYTNPFNCSCELLAFLRWLSAFPNRTSERMA
          TPN.FWECPNIENIDLSMNRIQ.LDG..F..L.KLTTCELYTNPFNCSCELL.F..WLS.FPNRT.ERM.
Retrocopy TPNAFWECPNIENIDLSMNRIQQLDGSTFTSLTKLTTCELYTNPFNCSCELLGFVKWLSVFPNRTNERMV

Parental  CDSPQGFFGYNLLSQNPRAASQRSALHVLGLVCTDDGSSVTSFYMIGTADSPTPPPDFASPCG-LDDCAS
          CDSP.G..GY.LLS.NP.....R.ALH.L..VCTDD...VT.F....T..S.TPPPD....CG.L.DC.S
Retrocopy CDSPPGVSGYSLLSPNPNNPTFRNALHMLTTVCTDD--YVTPFIPVPT-ESSTPPPDL-TLCG>LEDCPS

Parental  GTPPDEVINISPIFSDTKPVMVLKQVLHSTAVITVQIPQPYRKMYSLVLYNNSFYLDIQVLKNQREDIEL
          GT.P..............P.M.LKQV....A..TVQIP.P..KMY.L.LYNNSF..DIQ.LK...ED.EL
Retrocopy GTEPEDITISTYNVVEVNPLMKLKQVSNTGATVTVQIPHPFKKMYILSLYNNSFFSDIQTLKASKEDVEL

Parental  NNLKPNTDYTYCVASIRNSLRFNHTCLTISTGRRAGEDTTDNQSSATHYIMTILGCLFVMLLFLGLVVHC
          .NLKP.T.YTYCV.SIRNSLR.NHTCLTI.TG...G.....N...ATHYIMTILGCLF.M..FLG.V..C
Retrocopy KNLKPHTNYTYCVCSIRNSLRHNHTCLTITTGTLKGKARDVNNATATHYIMTILGCLFSMVIFLGVVYYC

Parental  LRKKRIMQEKERKMSRIQRTLIELKYGGEGDIEGGSGGSVAQK-LGAGESLSRMPYLPQGGEIDPYKLQE
          LR.KR...EK...........IELKYG.E...EG.......QK.L.AGES..RMPYLP...E...YK.QE
Retrocopy LRRKRQQDEKHKRAGSLKKNIIELKYGQE--LEGATVSRMSQKQLLAGESMARMPYLPSAAEMEQYKFQE

Parental  VVETPAHKPAKLNYMEVRG
          ...TP..K..K.NYM.VRG
Retrocopy MSDTP--KMMKGNYMDVRG

Legend:

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

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

Gasterosteus aculeatus was not studied using EST data.

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_19 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_19 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Oryzias latipes	retro_olat_18
Takifugu rubripes	retro_trub_13
Tetraodon nigroviridis	retro_tnig_5

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000016502	1 retrocopy	retro_gacu_19 ,
Oreochromis niloticus	ENSONIG00000000160	1 retrocopy	retro_onil_6,
Oryzias latipes	ENSORLG00000009720	1 retrocopy	retro_olat_18,
Tetraodon nigroviridis	ENSTNIG00000008254	1 retrocopy	retro_tnig_5,
Takifugu rubripes	ENSTRUG00000015197	1 retrocopy	retro_trub_13,
Xiphophorus maculatus	ENSXMAG00000014093	1 retrocopy	retro_xmac_1,