RetrogeneDB ID: retro_ttru_156

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1409:181666..182581(+)
• Located in intron of: ENSTTRG00000012290

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1L2
• Ensembl ID: ENSTTRG00000004505
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]

Sequence

>retro_ttru_156
GTGTCTAAGTCAGAGTCACCCAAAGAGCCCGAAGAGCTGTGGAAGCGCTGCATCGGAGGTTTGAGCTTTTGAAACAACCG
ATGACAGTCTGAGGAGCCATCGTGAGCAGGGGGAGCACTCACAGACTGTGTGGTAACGAGGGATCCAAGCACCAGGCGCT
CCAGAGACTTCGGGGTTGTCACGTGTGCCACTGTGGAGGAGGTGGATGCAGCCATGAAGGCAAGGCCACACGAGGTGGAT
GGAAGAGTTGGGGAACCAAAGAGGGCCGTCTCAAGAGAAGATTCTCGAAGACCTGGTGCCCACTTAACTGTGAAAAAGAT
TTTTGTTGGTGGCATTAAAGGAGACACTGAAGAACATCACCTAAGAGATTATTTTGAACAGTATGGGAAAACTGAAGTGA
TTGAAATCACGACTGACCGAGGCAGTGGCAAAAAGAGAGGCTTTGCTTTCGTAACCTTTGATGACCATGACTCTGTAGAC
AAGATTGTCATTCAGAAATACCACACTGTGAATGGCCACAACTGTGAAGTAAGGAAAGCCCTATCTCAGCAAGAGACGGC
TAGTGCCTCATCCAGCCAAAGAAGTCAAAGTGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGGGGTTTTGGTGGGAATG
ACAGCTTTGGTCGTGGAGGAAACTTCAGTGGTCGAGCTGGCTTTGGTGGCAGCTGCAGTGGTGGTGGATATGGTGGCAGT
GGGGATGGCTATAATGGATTTAGTAACAATGGAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTGGCAGTTACAA
CAATCAATCTTCAAATTTTGGAGGAAACTTTGGAGGCAGAAGTTCTGGCCCCTGTGGTGGTGGAGGCCAATACTTTGCCA
AACCCCCAAACCAAGGTGGCTGTGGTGGTTCCAGC

Alignment

ORF - retro_ttru_156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.21 %
• Parental protein coverage: 84.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLS-FETTDESLRSHFEQ-WGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV
          .SKSESPKEPE.L.K..IGGLS.FETTD.SLRSH.EQ..G.LTDCVV.RDP.T.RSR.FG.VT.ATVEEV
Retrocopy VSKSESPKEPEELWKRCIGGLS>FETTDDSLRSHREQ<GGALTDCVVTRDPSTRRSRDFGVVTCATVEEV

Parental  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT
          DAAM.ARPH.VDGRV.EPKRAVSREDS.RPGAHLTVKKIFVGGIK.DTEEHHLRDYFEQYGK.EVIEI.T
Retrocopy DAAMKARPHEVDGRVGEPKRAVSREDSRRPGAHLTVKKIFVGGIKGDTEEHHLRDYFEQYGKTEVIEITT

Parental  DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGG
          DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALS.QE.ASASSSQR..SGSGNFGGGRGG
Retrocopy DRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSQQETASASSSQRSQSGSGNFGGGRGG

Parental  GFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQG
          GFGGND.FGRGGNFSGR.GFGGS..GGGYGGSGDGYNGF.N.G...GGG..Y.......GS......N.G
Retrocopy GFGGNDSFGRGGNFSGRAGFGGSCSGGGYGGSGDGYNGFSNNGSNFGGGGSYN----DFGSYNNQSSNFG

Parental  SGYGGSDSYNNGRGGGGFGGGSGSNFGGGGS
          ...GG..S...G.GG..F.........GG.S
Retrocopy GNFGGRSSGPCGGGGQYFAKPPNQGGCGGSS

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_ttru_156 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DT660430	3415	3829	99.3	410	3	407

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_156 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,
Ictidomys tridecemlineatus	ENSSTOG00000006551	8 retrocopies	retro_itri_1291, retro_itri_1567, retro_itri_190, retro_itri_354, retro_itri_439, retro_itri_446, retro_itri_456, retro_itri_515,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,
Tursiops truncatus	ENSTTRG00000004505	27 retrocopies	retro_ttru_1202, retro_ttru_1223, retro_ttru_1251, retro_ttru_1331, retro_ttru_1362, retro_ttru_156 , retro_ttru_157, retro_ttru_1678, retro_ttru_1732, retro_ttru_1806, retro_ttru_1813, retro_ttru_1874, retro_ttru_221, retro_ttru_311, retro_ttru_479, retro_ttru_599, retro_ttru_605, retro_ttru_607, retro_ttru_620, retro_ttru_63, retro_ttru_678, retro_ttru_708, retro_ttru_812, retro_ttru_882, retro_ttru_902, retro_ttru_926, retro_ttru_981,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,