RetrogeneDB ID: retro_itri_354

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393286.1:2406190..2407078(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1L2
• Ensembl ID: ENSSTOG00000006551
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]

Sequence

>retro_itri_354
AAATCAGAGTCATGTAAAGTACCTGAACAGCTACGGAAGTTATTCATCATGGGGCTGAACTTTGGAACAACTGATGAAGA
GTCTGATATGCCATTTTGAGCAATGGGGAATGCTCAAGGACTGTATGGTAATGAGAGACCAAAACACCAAGCACTCCAGG
GGCTTTGGGTTTGTCACTTATGCCACTGTGGAGGGAGTGGATGCAGCTATGAATGAAAGACCACACAAGGTGAATGGAAC
AGTTATAGGACCAAAGAGAGTTGTCTCAAGAGAAGATTCTCAAAGACCAAAGACCCACTTAACTGTGAAAAAGATCTTTG
TTGGTGGCATTAAAGAAGACACTGAAGAACATCACCTATGGAATTATTTTGAACAGTATGGGAAAATTGAAGCTATTGCA
ATCATGACTAACCAAGACAATGGAAAGAAAAGGGGCTTTGCTTTTGTTACTTTCGATGACTATGACTCTGTGGATAAGAT
TGTTATTCAGAAATACCATATTGTGAATGGCCACAACTGAGAAATGAGGAAAGCCTTGTCAAAGCAAGAGATGTCTAGTG
CTTCATCTGGCCAAAGAGGCCGAGGTGGTTCTGGAAACTGGTGGTAGTTGTGGAGTTGGTGGAAAGAACAATTTTGGTAG
TGGAGGAAACTTCAGTGGCCATGGTGGCTTAAGGGCAACCATGGTAATGGATATGGTGGCAGCAGGATGGCTACAATGGA
TTTGATAATGATGATTGTTATGGAGGAGGTGGCCCTGGTTCTGAAAGAAGTAGAGGCTATGGAAGTGGTGGACAGGTTTA
TGGAAACTAGGGCAGTGGCTATGGCAGGAGGAGTAGCTATGACAGCTACAACAATGCAGGAGGCAGAAGTGGCTTTGGAG
GTGGTAGT

Alignment

ORF - retro_itri_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.16 %
• Parental protein coverage: 80.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KSESPKEPEQLRKLFIGGLSFETTDE-SLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA
          KSES.K.PEQLRKLFI.GL.F.TTDE.SL..HFEQWG.L.DC.VMRD.NTK.SRGFGFVTYATVE.VDAA
Retrocopy KSESCKVPEQLRKLFIMGLNFGTTDE>SLICHFEQWGMLKDCMVMRDQNTKHSRGFGFVTYATVEGVDAA

Parental  MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG
          MN.RPHKV.G.V..PKR.VSREDSQRP..HLTVKKIFVGGIKEDTEEHHL..YFEQYGKIE.I.IMT...
Retrocopy MNERPHKVNGTVIGPKRVVSREDSQRPKTHLTVKKIFVGGIKEDTEEHHLWNYFEQYGKIEAIAIMTNQD

Parental  SGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGG-GRGGGF
          .GKKRGFAFVTFDD.DSVDKIVIQKYH.VNGHN.E.RKALSKQEM.SASS.QR...G.G..G..G...G.
Retrocopy NGKKRGFAFVTFDDYDSVDKIVIQKYHIVNGHN*EMRKALSKQEMSSASSGQR---GRGGSGN>GGSCGV

Parental  GGNDNFGRGGNFSGRGG-FGGSRGGGGYGGS-GDGYNGFGNDGGYGGGGGPGYSGGSRGYGSGGQGYGNQ
          GG..NFG.GGNFSG.GG...G..G..GYGGS..DGYNGF.ND..Y.GGGGPG.S..SRGYGSGGQ.YGN.
Retrocopy GGKNNFGSGGNFSGHGG<LKGNHG-NGYGGS<QDGYNGFDNDDCY-GGGGPG-SERSRGYGSGGQVYGN*

Parental  GSGYGGSGSYDSYNNGGGGGGFGGGS
          GSGYG...SYDSYNN.GG..GFGGGS
Retrocopy GSGYGRRSSYDSYNNAGGRSGFGGGS

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_354 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_354 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 11 parental genes, and 60 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	ENSSTOG00000006202	3 retrocopies	retro_itri_1723, retro_itri_448, retro_itri_717,
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,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
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,