RetrogeneDB ID: retro_itri_880

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393337.1:7731959..7732484(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB2
• Ensembl ID: ENSSTOG00000023980
• Aliases: None
• Description: high mobility group box 2 [Source:HGNC Symbol;Acc:5000]

Sequence

>retro_itri_880
ATGGGTAAGGGAGAGCCCACTAAGCCCCAAAGGGCAAAATGCCTTTGTACCGACCTGACAGGAAGAGCACAAGAAGAAAC
AACCAGGCTCTACCGTCAACTTCACTGAACTCTCCAAGAAATGCTTGGAGAGATGGAAGACCATGTCTGCCAAGGAAAAT
CGAAGTTTGAAGATATGGGGAAAAAAAGTAACAAAGCTCAATGTTACAGGGAGATGAAGAATTAGGTTCCCCTCAAAGGT
GATAAGAAAAGGAAGAAAAAAGATCCCAATGCTCCTAAGAGACCACCATCTGCCTTCTTTCAATTTTGCTGTGAGCATCG
CCCAAAGACCGATGAACACCCAGGCTTGTCCACCGGGGATACTGCAAACAAACTGGGTGAAATGTGGTCTGAGCACTCAG
CCAGGGATACACAGGCATGTGAACAAAAAGCGGATAAGCTAAAGGAGCGGCATGAAAAGCGTATTGTGCATACCCCGCTA
AGGGCGCAGTGAAGCAGGAGGAAGGGCCCTGGTAGGGCAGCAGGC

Alignment

ORF - retro_itri_880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.43 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPNK-PRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKE-KSKFEDMAK-SD
          MGKG.P.K.P.G.......FV.T..EEHKKK.P.S.VNF.E.SKKC.ERWKTMSAKE.KSKFEDM.K.S.
Retrocopy MGKGEPTK>PKGQNA----FVPT*QEEHKKKQPGSTVNFTELSKKCLERWKTMSAKE<KSKFEDMGKKSN

Parental  KARYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQS
          KA...REMKN.VP.KGDKK.KKKDPNAPKRPPSAFF.FC.EHRPK...EHPGLS.GDTA.KLGEMWSE.S
Retrocopy KAQCYREMKN*VPLKGDKKRKKKDPNAPKRPPSAFFQFCCEHRPK-TDEHPGLSTGDTANKLGEMWSEHS

Parental  AKDKQPYEQKAAKLKEKYEKDI-AAYRAK-GKSEAG-KKGPGRPTG
          A.D.Q..EQKA.KLKE..EK.I..AY.AK.G.SEAG..KGPGR..G
Retrocopy ARDTQACEQKADKLKERHEKRI<CAYPAK<GRSEAG<RKGPGRAAG

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_880 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_880 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 23 parental genes, and 100 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015101	1 retrocopy	retro_btau_58,
Callithrix jacchus	ENSCJAG00000005112	2 retrocopies	retro_cjac_2555, retro_cjac_832,
Dasypus novemcinctus	ENSDNOG00000019440	4 retrocopies	retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Echinops telfairi	ENSETEG00000010379	3 retrocopies	retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi	ENSETEG00000016379	1 retrocopy	retro_etel_414,
Felis catus	ENSFCAG00000004218	2 retrocopies	retro_fcat_279, retro_fcat_52,
Homo sapiens	ENSG00000164104	1 retrocopy	retro_hsap_3663,
Gorilla gorilla	ENSGGOG00000015882	1 retrocopy	retro_ggor_2474,
Loxodonta africana	ENSLAFG00000010417	3 retrocopies	retro_lafr_1096, retro_lafr_1142, retro_lafr_595,
Macropus eugenii	ENSMEUG00000002256	3 retrocopies	retro_meug_1920, retro_meug_1989, retro_meug_550,
Myotis lucifugus	ENSMLUG00000026303	4 retrocopies	retro_mluc_1113, retro_mluc_1381, retro_mluc_1726, retro_mluc_2011,
Monodelphis domestica	ENSMODG00000003527	3 retrocopies	retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Mustela putorius furo	ENSMPUG00000001919	9 retrocopies	retro_mputfur_1134, retro_mputfur_1167, retro_mputfur_1379, retro_mputfur_1475, retro_mputfur_1631, retro_mputfur_1633, retro_mputfur_1644, retro_mputfur_940, retro_mputfur_989,
Mus musculus	ENSMUSG00000054717	23 retrocopies	retro_mmus_1477, retro_mmus_1745, retro_mmus_1974, retro_mmus_1975, retro_mmus_2269, retro_mmus_2527, retro_mmus_2528, retro_mmus_2529, retro_mmus_2530, retro_mmus_2531, retro_mmus_2843, retro_mmus_2884, retro_mmus_3248, retro_mmus_3426, retro_mmus_461, retro_mmus_626, retro_mmus_642, retro_mmus_796, retro_mmus_861, retro_mmus_901, retro_mmus_902, retro_mmus_904, retro_mmus_905,
Nomascus leucogenys	ENSNLEG00000006662	3 retrocopies	retro_nleu_113, retro_nleu_517, retro_nleu_550,
Oryctolagus cuniculus	ENSOCUG00000000074	1 retrocopy	retro_ocun_1829,
Pongo abelii	ENSPPYG00000015204	3 retrocopies	retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes	ENSPTRG00000016597	3 retrocopies	retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Rattus norvegicus	ENSRNOG00000013167	2 retrocopies	retro_rnor_173, retro_rnor_54,
Ictidomys tridecemlineatus	ENSSTOG00000000443	19 retrocopies	retro_itri_1060, retro_itri_1220, retro_itri_127, retro_itri_1489, retro_itri_1531, retro_itri_1580, retro_itri_1644, retro_itri_1852, retro_itri_233, retro_itri_238, retro_itri_444, retro_itri_518, retro_itri_553, retro_itri_584, retro_itri_712, retro_itri_754, retro_itri_792, retro_itri_825, retro_itri_991,
Ictidomys tridecemlineatus	ENSSTOG00000023908	6 retrocopies	retro_itri_1366, retro_itri_1527, retro_itri_1655, retro_itri_1749, retro_itri_777, retro_itri_909,
Ictidomys tridecemlineatus	ENSSTOG00000023980	2 retrocopies	retro_itri_1720, retro_itri_880 ,
Tursiops truncatus	ENSTTRG00000015650	1 retrocopy	retro_ttru_1640,