RetrogeneDB ID: retro_amel_258

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192368.1:3289710..3290213(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000018099
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHB
• Ensembl ID: ENSAMEG00000012364
• Aliases: None
• Description: None

Sequence

>retro_amel_258
CCGCATCTTCACCAGCATCGGGGAGACTACGATGAGCGGGTGCTGCCGTCCATCACCACGGAGATCCTCAAGTCGGTGGT
GGCTCGCTTTGATGCTGGAGAACTGATCACCCAGAGAGAGCTGGTCTCCAGACAGGTGAGCGATGACCTCACGGAGCGAG
CAGCCACCTTTGGGCTCATCCTGGATGACGTGTCCTTGACGCATCTGACCTTCGGGAAGGAGTTCACAGAGCGGTGGAAG
CCAAGCAGGTGGCTCAGCAGGAAGCAGAGACGGCCAGGTTCGTGGTGGAGAAGGCTGAGCAGCAGAAGAAGGCGGCCATC
ATCTCCGCGGAGGGCGACACCAAGGCCGCCAAGCTGATCGCCAACTCACTCGCCACTGCGGGCGATGGCCTCACGGAGCT
GCGCAAGCTGGAGGCCGCCGAGGACATCGCGTACCAGCTGTCGCACTCTCGGAACATCACCTACCTGCCGGCTGGGCAGT
CCGTACTCCTGCAGCTGCCCCAG

Alignment

ORF - retro_amel_258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.9 %
• Parental protein coverage: 61.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRIFTSIGDYDERVLPSITTEILKSVVARFDAGELITQRELVSRQVSDDLTERAATFGLILDDVSLTHLT
          P......GDYDERVLPSITTEILKSVVARFDAGELITQRELVSRQVSDDLTERAATFGLILDDVSLTHLT
Retrocopy PHLHQHRGDYDERVLPSITTEILKSVVARFDAGELITQRELVSRQVSDDLTERAATFGLILDDVSLTHLT

Parental  FGKEFTE-AVEAKQVAQQEAERARFVVEKAEQQKKAAIISAEGDSKAAELIANSLATAGDGLIELRKLEA
          FGKEFTE.AVEAKQVAQQEAE.ARFVVEKAEQQKKAAIISAEGD.KAA.LIANSLATAGDGL.ELRKLEA
Retrocopy FGKEFTE<AVEAKQVAQQEAETARFVVEKAEQQKKAAIISAEGDTKAAKLIANSLATAGDGLTELRKLEA

Parental  AEDIAYQLSRSRNITYLPAGQSVLLQLPQ
          AEDIAYQLS.SRNITYLPAGQSVLLQLPQ
Retrocopy AEDIAYQLSHSRNITYLPAGQSVLLQLPQ

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_258 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_258 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 15 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004797	1 retrocopy	retro_acar_49,
Ailuropoda melanoleuca	ENSAMEG00000012364	1 retrocopy	retro_amel_258 ,
Choloepus hoffmanni	ENSCHOG00000007588	2 retrocopies	retro_chof_1159, retro_chof_2193,
Callithrix jacchus	ENSCJAG00000007174	22 retrocopies	retro_cjac_1048, retro_cjac_1403, retro_cjac_1683, retro_cjac_1761, retro_cjac_1820, retro_cjac_2261, retro_cjac_2389, retro_cjac_2390, retro_cjac_2391, retro_cjac_2445, retro_cjac_2523, retro_cjac_2659, retro_cjac_2663, retro_cjac_2909, retro_cjac_4205, retro_cjac_570, retro_cjac_635, retro_cjac_662, retro_cjac_872, retro_cjac_937, retro_cjac_966, retro_cjac_980,
Erinaceus europaeus	ENSEEUG00000006481	3 retrocopies	retro_eeur_219, retro_eeur_285, retro_eeur_369,
Homo sapiens	ENSG00000167085	15 retrocopies	retro_hsap_1113, retro_hsap_1514, retro_hsap_161, retro_hsap_1640, retro_hsap_2170, retro_hsap_2692, retro_hsap_3534, retro_hsap_3750, retro_hsap_3868, retro_hsap_3869, retro_hsap_4186, retro_hsap_4888, retro_hsap_517, retro_hsap_617, retro_hsap_776,
Gorilla gorilla	ENSGGOG00000028002	12 retrocopies	retro_ggor_124, retro_ggor_1722, retro_ggor_1876, retro_ggor_238, retro_ggor_2387, retro_ggor_246, retro_ggor_2607, retro_ggor_3053, retro_ggor_476, retro_ggor_643, retro_ggor_741, retro_ggor_870,
Macropus eugenii	ENSMEUG00000005122	1 retrocopy	retro_meug_708,
Myotis lucifugus	ENSMLUG00000008203	2 retrocopies	retro_mluc_116, retro_mluc_2190,
Macaca mulatta	ENSMMUG00000000156	13 retrocopies	retro_mmul_1096, retro_mmul_1119, retro_mmul_1165, retro_mmul_1425, retro_mmul_151, retro_mmul_1565, retro_mmul_2148, retro_mmul_2420, retro_mmul_426, retro_mmul_521, retro_mmul_834, retro_mmul_866, retro_mmul_933,
Monodelphis domestica	ENSMODG00000012210	1 retrocopy	retro_mdom_812,
Otolemur garnettii	ENSOGAG00000027015	1 retrocopy	retro_ogar_968,
Procavia capensis	ENSPCAG00000008851	1 retrocopy	retro_pcap_74,
Pan troglodytes	ENSPTRG00000009376	14 retrocopies	retro_ptro_1025, retro_ptro_1110, retro_ptro_154, retro_ptro_1656, retro_ptro_1817, retro_ptro_2401, retro_ptro_2545, retro_ptro_2841, retro_ptro_2964, retro_ptro_3256, retro_ptro_386, retro_ptro_451, retro_ptro_542, retro_ptro_686,
Rattus norvegicus	ENSRNOG00000046799	18 retrocopies	retro_rnor_1058, retro_rnor_1416, retro_rnor_1540, retro_rnor_1542, retro_rnor_2398, retro_rnor_2399, retro_rnor_2610, retro_rnor_2653, retro_rnor_2815, retro_rnor_2826, retro_rnor_2848, retro_rnor_2855, retro_rnor_2909, retro_rnor_292, retro_rnor_2948, retro_rnor_2949, retro_rnor_543, retro_rnor_898,