RetrogeneDB ID: retro_ttru_479

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2419:172803..173557(+)
• Located in intron of: ENSTTRG00000016689

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_479
AGTCAGTCTCCCAAAGAGCCCGAACAGCTGCAGAAGCTCCTCATCAGACGTCTGAGCTTTGAAACAATTGATGCGAATCT
GAGGAGCCACCTGAGCAGCGGGCAGCGCTCACAGACTGTGTGGTAACGAGGGGTCCAAACACCAGGTGCTCCAGAGGCTT
CGGGTTTGTCACGTATGCCATTGCAGAGGAGGTGGATGCGGCCATGGATGCGAGGCCACACGAGGTGGATGGAAGAGTTG
GGGAACCAAAGAGGGCCGTCTCAAGAGAAGATTCTCAAAGACCTGGTGCCCACTTAACCGTGAAAAAAATTTTTGTTGGT
GGCATTAAAGAAGACACTGAAGAACATCACCTAAGAGATTATTTTGAACAGTATGGGAGAACTGAAGTGATTGAAATCAT
GACCGACTGAGGCAGTGGCAAAACAGAGGCTTTGCTTTTGTAACCTTTGATGACCATGACGCCGCAGACAAGACTGTCAT
TCAGAAATATCACACAGTGAACGGCCACAACTGTGAAGTAAGGAAAGCCCTATCTAAGCAAGAGAAGGCTAGCGCTTCAT
CCAGCCAAAGAGGTCGAAGTGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGGGGTTTTGGTGGGAATGACAACTCTGCT
CGTGGAGGGAACGTCAGTGGTCGAGATGCCTTTGGTGGCAGCCGTGGTGGGGGGGGATATGGTGGCAGTGGGGATGGCAG
TAATGGATTTGGTAATGACGGAAGCCATTTTGGA

Alignment

ORF - retro_ttru_479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.07 %
• Parental protein coverage: 68.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SESPKEPEQLRKLFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM
          S.SPKEPEQL.KL.I..LSFET.D..LRSH..EQ...LTDCVV.R.PNT..SRGFGFVTYA..EEVDAAM
Retrocopy SQSPKEPEQLQKLLIRRLSFETIDANLRSHL<EQRAALTDCVVTRGPNTRCSRGFGFVTYAIAEEVDAAM

Parental  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS
          .ARPH.VDGRV.EPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG..EVIEIMTD.GS
Retrocopy DARPHEVDGRVGEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGRTEVIEIMTD*GS

Parental  GK-KRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFG
          GK..RGFAFVTFDDHD..DK.VIQKYHTVNGHNCEVRKALSKQE.ASASSSQRGRSGSGNFGGGRGGGFG
Retrocopy GK<NRGFAFVTFDDHDAADKTVIQKYHTVNGHNCEVRKALSKQEKASASSSQRGRSGSGNFGGGRGGGFG

Parental  GNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGG
          GNDN..RGGN.SGR..FGGSRG...YGGSGDG.NGFGNDG...G
Retrocopy GNDNSARGGNVSGRDAFGGSRGXXXYGGSGDGSNGFGNDGSHFG

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

No EST(s) were mapped for retro_ttru_479 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_479 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.

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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,